[20] Tangye SG, Avery DT, Hodgkin PDA. Division-linked mechanism for the rapid generation of Ig-secreting cells from human memory B cells. Journal of Immunology. 2003;170(1):261-269 [21] Oettinger MA, Schatz DG, Gorka C, Baltimore D. RAG-1 and RAG-2, adjacent genes that synergistically activate V(D)J recombination. Science. 1990;248(4962):1517-1523 [22] Schatz DG, Oettinger MA, Baltimore D. The V(D)J recombination activating gene, RAG-1.

[23] Stavnezer J, Guikema JE, Schrader CE. Mechanism and regulation of class switch

[24] Muramatsu M, Kinoshita K, Fagarasan S, Yamada S, Shinkai Y, Honjo T. Class switch recombination and hypermutation require activation-induced cytidine deaminase (AID),

[25] Okazaki IM, Kinoshita K, Muramatsu M, Yoshikawa K, Honjo T. The AID enzyme induces class switch recombination in fibroblasts. Nature. 2002;416(6878):340-345 [26] Fear DJ. Mechanisms regulating the targeting and activity of activation induced cytidine

[27] Dudley DD, Chaudhuri J, Bassing CH, Alt FW. Mechanism and control of V(D)J recombination versus class switch recombination: Similarities and differences. Advances in

[28] Manis JP, Tian M, Alt FW. Mechanism and control of class-switch recombination. Trends

[29] Chowdhury M, Forouhi O, Dayal S, McCloskey N, Gould HJ, Felsenfeld G, et al. Analysis of intergenic transcription and histone modification across the human immunoglobulin heavy-chain locus. Proceedings of the National Academy of Sciences of the United

[30] Jeppson JD, Patel HR, Sakata N, Domenico J, Terada N, Gelfand EW. Requirement for dual signals by anti-CD40 and IL-4 for the induction of nuclear factor-kappa B, IL-6, and

[31] Zhang Y, Fear DJ, Willis-Owen SA, Cookson WO, Moffatt MF. Global gene regulation during activation of immunoglobulin class switching in human B cells. Scientific Reports.

[32] Itoh-Nakadai A, Hikota R, Muto A, Kometani K, Watanabe-Matsui M, Sato Y, et al. The transcription repressors Bach2 and Bach1 promote B cell development by repressing the

myeloid program. Nature Immunology. 2014;15(12):1171-1180

IgE in human B lymphocytes. Journal of Immunology. 1998;161(4):1738-1742

naive B cells. Journal of Immunology. 2009;182(2):890-901

recombination. Annual Review of Immunology. 2008;26:261-292

deaminase. Current Opinion in Immunology. 2013;25(5):619-628

a potential RNA editing enzyme. Cell. 2000;102(5):553-563

2005;35(12):3433-3441

Cell. 1989;59(6):1035-1048

Immunology. 2005;86:43-112

2016;6:37988

in Immunology. 2002;23(1):31-39

States of America. 2008;105(41):15872-15877

[18] Wirths S, Lanzavecchia A. ABCB1 transporter discriminates human resting naive B cells from cycling transitional and memory B cells. European Journal of Immunology. 2005;35(12):3433-3441

[3] Ribatti D, Crivellato E, Vacca A. The contribution of Bruce Glick to the definition of the role played by the bursa of Fabricius in the development of the B cell lineage. Clinical

[4] Welner RS, Pelayo R, Kincade PW. Evolving views on the genealogy of B cells. Nature

[5] Harris DP, Goodrich S, Mohrs K, Mohrs M, Lund FE. Cutting edge: The development of IL-4-producing B cells (B effector 2 cells) is controlled by IL-4, IL-4 receptor alpha, and

[6] Harris DP, Goodrich S, Gerth AJ, Peng SL, Lund FE. Regulation of IFN-gamma production by B effector 1 cells: Essential roles for T-bet and the IFN-gamma receptor. Journal

[7] Lin YC, Jhunjhunwala S, Benner C, Heinz S, Welinder E, Mansson R, et al. A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell

[8] Tonegawa S. Somatic generation of antibody diversity. Nature. 1983;302(5909):575-581 [9] Nemazee D. Mechanisms of central tolerance for B cells. Nature Reviews Immunology.

[10] Pascual V, Liu YJ, Magalski A, de Bouteiller O, Banchereau J, Capra JD. Analysis of somatic mutation in five B cell subsets of human tonsil. The Journal of Experimental

[11] Allen CD, Okada T, Cyster JG. Germinal-center organization and cellular dynamics.

[12] Good-Jacobson KL, Shlomchik MJ. Plasticity and heterogeneity in the generation of memory B cells and long-lived plasma cells: The influence of germinal center interac-

[13] Hauser AE, Junt T, Mempel TR, Sneddon MW, Kleinstein SH, Henrickson SE, et al. Definition of germinal-center B cell migration in vivo reveals predominant intrazonal

[14] Batista FD, Harwood NE. The who, how and where of antigen presentation to B cells.

[15] Okada T, Miller MJ, Parker I, Krummel MF, Neighbors M, Hartley SB, et al. Antigenengaged B cells undergo chemotaxis toward the T zone and form motile conjugates with

[16] Kerfoot SM, Yaari G, Patel JR, Johnson KL, Gonzalez DG, Kleinstein SH, et al. Germinal center B cell and T follicular helper cell development initiates in the interfollicular zone.

[17] Kaminski DA, Wei C, Qian Y, Rosenberg AF, Sanz I. Advances in human B cell pheno-

tions and dynamics. Journal of Immunology. 2010;185(6):3117-3125

circulation patterns. Immunity. 2007;26(5):655-667

Nature Reviews Immunology. 2009;9(1):15-27

helper T cells. PLoS Biology. 2005;3(6):e150

typic profiling. Frontiers in Immunology. 2012;3:302

Immunity. 2011;34(6):947-960

and Experimental Immunology. 2006;145(1):1-4

180 Gene Expression and Regulation in Mammalian Cells - Transcription From General Aspects

Th2 cells. Journal of Immunology. 2005;175(11):7103-7107

Reviews Immunology. 2008;8(2):95-106

of Immunology. 2005;174(11):6781-6790

2017;17(5):281-294

Medicine. 1994;180(1):329-339

Immunity. 2007;27(2):190-202

fate. Nature Immunology. 2010;11(7):635-643

[33] Oyake T, Itoh K, Motohashi H, Hayashi N, Hoshino H, Nishizawa M, et al. Bach proteins belong to a novel family of BTB-basic leucine zipper transcription factors that interact with MafK and regulate transcription through the NF-E2 site. Molecular and Cellular Biology. 1996;16(11):6083-6095

[46] Chiu R, Boyle WJ, Meek J, Smeal T, Hunter T, Karin M. The c-Fos protein interacts with c-Jun/AP-1 to stimulate transcription of AP-1 responsive genes. Cell. 1988;54(4):541-

Gene Expression during the Activation of Human B Cells http://dx.doi.org/10.5772/intechopen.71863 183

[47] Davis BJ, Flanagan BF, Gilfillan AM, Metcalfe DD, Coleman JW. Nitric oxide inhibits IgE-dependent cytokine production and Fos and Jun activation in mast cells. Journal of

[48] Lewin I, Jacob-Hirsch J, Zang ZC, Kupershtein V, Szallasi Z, Rivera J, et al. Aggregation of the Fc epsilon RI in mast cells induces the synthesis of Fos-interacting protein and increases its DNA binding-activity: The dependence on protein kinase C-beta. The

[49] Zhao J, Harper R, Barchowsky A, Di YP. Identification of multiple MAPK-mediated transcription factors regulated by tobacco smoke in airway epithelial cells. American Journal of Physiology Lung Cellular and Molecular Physiology. 2007;293(2):L480-L490

[50] Papin JA, Palsson BO. The JAK-STAT signaling network in the human B-cell: An

[51] Pollock R, Treisman R. Human SRF-related proteins: DNA-binding properties and

[52] Wang L, Kurosaki T, Corey SJ. Engagement of the B-cell antigen receptor activates STAT through Lyn in a Jak-independent pathway. Oncogene. 2007;26(20):2851-2859

[53] Mittrucker HW, Matsuyama T, Grossman A, Kundig TM, Potter J, Shahinian A, et al. Requirement for the transcription factor LSIRF/IRF4 for mature B and T lymphocyte

[54] Todd DJ, McHeyzer-Williams LJ, Kowal C, Lee AH, Volpe BT, Diamond B, et al. XBP1 governs late events in plasma cell differentiation and is not required for antigen-specific memory B cell development. The Journal of Experimental Medicine. 2009;206(10):2151-

[55] Ise W, Kohyama M, Schraml BU, Zhang T, Schwer B, Basu U, et al. The transcription factor BATF controls the global regulators of class-switch recombination in both B cells

[56] Kashiwada M, Levy DM, McKeag L, Murray K, Schroder AJ, Canfield SM, et al. IL-4 induced transcription factor NFIL3/E4BP4 controls IgE class switching. Proceedings of the National Academy of Sciences of the United States of America. 2010;107(2):821-826

[57] Bie Q, Jin C, Zhang B, Dong H. IL-17B: A new area of study in the IL-17 family. Molecular

[58] Wang H, Mobini R, Fang Y, Barrenas F, Zhang H, Xiang Z, et al. Allergen challenge of peripheral blood mononuclear cells from patients with seasonal allergic rhinitis increases IL-17RB, which regulates basophil apoptosis and degranulation. Clinical and Experimental Allergy: Journal of the British Society for Allergy and Clinical Immunol-

extreme signaling pathway analysis. Biophysical Journal. 2004;87(1):37-46

potential regulatory targets. Genes & Development. 1991;5(12A):2327-2341

552

2159

Immunology. 2004;173(11):6914-6920

function. Science. 1997;275(5299):540-543

Immunology. 2017;90:50-56

ogy. 2010;40(8):1194-1202

and T cells. Nature Immunology. 2011;12(6):536-543

Journal of Biological Chemistry. 1996;271(3):1514-1519

[46] Chiu R, Boyle WJ, Meek J, Smeal T, Hunter T, Karin M. The c-Fos protein interacts with c-Jun/AP-1 to stimulate transcription of AP-1 responsive genes. Cell. 1988;54(4):541- 552

[33] Oyake T, Itoh K, Motohashi H, Hayashi N, Hoshino H, Nishizawa M, et al. Bach proteins belong to a novel family of BTB-basic leucine zipper transcription factors that interact with MafK and regulate transcription through the NF-E2 site. Molecular and

[34] Muto A, Tashiro S, Nakajima O, Hoshino H, Takahashi S, Sakoda E, et al. The transcriptional programme of antibody class switching involves the repressor Bach2. Nature.

[35] Muto A, Ochiai K, Kimura Y, Itoh-Nakadai A, Calame KL, Ikebe D, et al. Bach2 represses plasma cell gene regulatory network in B cells to promote antibody class switch. The

[36] McManus S, Ebert A, Salvagiotto G, Medvedovic J, Sun Q, Tamir I, et al. The transcription factor Pax5 regulates its target genes by recruiting chromatin-modifying proteins in

[37] Schwenzer R, Siemienski K, Liptay S, Schubert G, Peters N, Scheurich P, et al. The human tumor necrosis factor (TNF) receptor-associated factor 1 gene (TRAF1) is upregulated by cytokines of the TNF ligand family and modulates TNF-induced activation of NF-kappaB and c-Jun N-terminal kinase. The Journal of Biological Chemistry.

[38] Werfel T, Heratizadeh A, Niebuhr M, Kapp A, Roesner LM, Karch A, et al. Exacerbation of atopic dermatitis on grass pollen exposure in an environmental challenge chamber.

[39] Abelius MS, Ernerudh J, Berg G, Matthiesen L, Nilsson LJ, Jenmalm MC. High cord blood levels of the T-helper 2-associated chemokines CCL17 and CCL22 precede allergy development during the first 6 years of life. Pediatric Research. 2011;70(5):495-500 [40] Perros F, Hoogsteden HC, Coyle AJ, Lambrecht BN, Hammad H. Blockade of CCR4 in a humanized model of asthma reveals a critical role for DC-derived CCL17 and CCL22 in attracting Th2 cells and inducing airway inflammation. Allergy. 2009;64(7):995-1002 [41] Hai T, Curran T. Cross-family dimerization of transcription factors Fos/Jun and ATF/ CREB alters DNA binding specificity. Proceedings of the National Academy of Sciences

[42] Lee W, Mitchell P, Tjian R. Purified transcription factor AP-1 interacts with TPA-

[43] Zhou H, Zarubin T, Ji Z, Min Z, Zhu W, Downey JS, et al. Frequency and distribution of AP-1 sites in the human genome. DNA Research: An International Journal for Rapid

[44] Karin M, Liu Z, Zandi E. AP-1 function and regulation. Current Opinion in Cell Biology.

[45] Gustems M, Woellmer A, Rothbauer U, Eck SH, Wieland T, Lutter D, et al. c-Jun/c-Fos heterodimers regulate cellular genes via a newly identified class of methylated DNA

The Journal of Allergy and Clinical Immunology. 2015;136(1):96-103 e9

of the United States of America. 1991;88(9):3720-3724

inducible enhancer elements. Cell. 1987;49(6):741-752

Publication of Reports on Genes and Genomes. 2005;12(2):139-150

sequence motifs. Nucleic Acids Research. 2014;42(5):3059-3072

committed B cells. The EMBO Journal. 2011;30(12):2388-2404

Cellular Biology. 1996;16(11):6083-6095

182 Gene Expression and Regulation in Mammalian Cells - Transcription From General Aspects

EMBO Journal. 2010;29(23):4048-4061

2004;429(6991):566-571

1999;274(27):19368-19374

1997;9(2):240-246

[59] Hunninghake GM, Chu JH, Sharma SS, Cho MH, Himes BE, Rogers AJ, et al. The CD4+ T-cell transcriptome and serum IgE in asthma: IL17RB and the role of sex. BMC Pulmonary Medicine. 2011;11:17

[73] Cunninghame Graham DS, Graham RR, Manku H, Wong AK, Whittaker JC, Gaffney PM, et al. Polymorphism at the TNF superfamily gene TNFSF4 confers susceptibility to

Gene Expression during the Activation of Human B Cells http://dx.doi.org/10.5772/intechopen.71863 185

[74] Gourh P, Arnett FC, Tan FK, Assassi S, Divecha D, Paz G, et al. Association of TNFSF4 (OX40L) polymorphisms with susceptibility to systemic sclerosis. Annals of the Rheu-

[75] Sun X, Haider Ali MSS, Moran M. The role of interactions of long non-coding RNAs and heterogeneous nuclear ribonucleoproteins in regulating cellular functions. The Biochem-

[76] Chung MC, Kim HK, Kawamoto S. TFEC can function as a transcriptional activator of the nonmuscle myosin II heavy chain—A gene in transfected cells. Biochemistry. 2001;

[77] Zhao GQ, Zhao Q, Zhou X, Mattei MG, de Crombrugghe B. TFEC, a basic helix-loophelix protein, forms heterodimers with TFE3 and inhibits TFE3-dependent transcription

[78] Mahony CB, Fish RJ, Pasche C, Bertrand JY. tfec controls the hematopoietic stem cell vascular niche during zebrafish embryogenesis. Blood. 2016;128(10):1336-1345

[79] Moriggi G, Nieto B, Dosil M. Rrp12 and the Exportin Crm1 participate in late assembly events in the nucleolus during 40S ribosomal subunit biogenesis. PLoS Genetics. 2014;

[80] Yang SH, Jung HJ, Coffinier C, Fong LG, Young SG. Are B-type lamins essential in all

[81] Bolotin E, Armendariz A, Kim K, Heo SJ, Boffelli D, Tantisira K, et al. Statin-induced changes in gene expression in EBV-transformed and native B-cells. Human Molecular

[82] Ranuncolo SM, Polo JM, Melnick A. BCL6 represses CHEK1 and suppresses DNA damage pathways in normal and malignant B-cells. Blood Cells, Molecules & Diseases.

[83] Ly LL, Yoshida H, Yamaguchi M. Nuclear transcription factor Y and its roles in cellular processes related to human disease. American Journal of Cancer Research. 2013;3(4):339-346

[84] Corson TW, Huang A, Tsao MS, Gallie BL. KIF14 is a candidate oncogene in the 1q minimal region of genomic gain in multiple cancers. Oncogene. 2005;24(30):4741-4753

[85] Jiang W, Jimenez G, Wells NJ, Hope TJ, Wahl GM, Hunter T, et al. PRC1: A human mitotic spindle-associated CDK substrate protein required for cytokinesis. Molecular

[86] Tang H, Xiao G, Behrens C, Schiller J, Allen J, Chow CW, et al. A 12-gene set predicts survival benefits from adjuvant chemotherapy in non-small cell lung cancer patients.

systemic lupus erythematosus. Nature Genetics. 2008;40(1):83-89

activation. Molecular and Cellular Biology. 1993;13(8):4505-4512

matic Diseases. 2010;69(3):550-555

ical Journal. 2017;474(17):2925-2935

mammalian cells? Nucleus. 2011;2(6):562-569

Genetics. 2014;23(5):1202-1210

40(30):8887-8897

10(12):e1004836

2008;41(1):95-99

Cell. 1998;2(6):877-885

[73] Cunninghame Graham DS, Graham RR, Manku H, Wong AK, Whittaker JC, Gaffney PM, et al. Polymorphism at the TNF superfamily gene TNFSF4 confers susceptibility to systemic lupus erythematosus. Nature Genetics. 2008;40(1):83-89

[59] Hunninghake GM, Chu JH, Sharma SS, Cho MH, Himes BE, Rogers AJ, et al. The CD4+ T-cell transcriptome and serum IgE in asthma: IL17RB and the role of sex. BMC Pulmo-

[60] Jung JS, Park BL, Cheong HS, Bae JS, Kim JH, Chang HS, et al. Association of IL-17RB

[61] Lefebvre C, Rajbhandari P, Alvarez MJ, Bandaru P, Lim WK, Sato M, et al. A human Bcell interactome identifies MYB and FOXM1 as master regulators of proliferation in

[62] Reinberg A, Gervais P, Levi F, Smolensky M, Del Cerro L, Ugolini C. Circadian and circannual rhythms of allergic rhinitis: An epidemiologic study involving chronobiologic methods. The Journal of Allergy and Clinical Immunology. 1988;81(1):51-62 [63] Kelly EA, Houtman JJ, Jarjour NN. Inflammatory changes associated with circadian variation in pulmonary function in subjects with mild asthma. Clinical and Experimental Allergy: Journal of the British Society for Allergy and Clinical Immunology. 2004;

[64] Maurer M, Ortonne JP, Zuberbier T. Chronic urticaria: An internet survey of health behaviours, symptom patterns and treatment needs in European adult patients. The

[65] Nakamura Y, Harama D, Shimokawa N, Hara M, Suzuki R, Tahara Y, et al. Circadian clock gene Period2 regulates a time-of-day-dependent variation in cutaneous anaphylactic reaction. The Journal of Allergy and Clinical Immunology. 2011;127(4):1038-45 e1-3. [66] Sun H, Lu B, Li RQ, Flavell RA, Taneja R, Defective T. Cell activation and autoimmune disorder in Stra13-deficient mice. Nature Immunology. 2001;2(11):1040-1047

[67] Yu X, Rollins D, Ruhn KA, Stubblefield JJ, Green CB, Kashiwada M, et al. TH17 cell differentiation is regulated by the circadian clock. Science. 2013;342(6159):727-730 [68] Nakada M, Hayashi Y, Hamada J. Role of Eph/ephrin tyrosine kinase in malignant

[69] Gucciardo E, Sugiyama N, Lehti K. Eph- and ephrin-dependent mechanisms in tumor and stem cell dynamics. Cellular and Molecular Life Sciences: CMLS. 2014;71(19):3685-3710

[70] Wei W, Wang H, Ji S. Paradoxes of the EphB1 receptor in malignant brain tumors.

[71] Davis S, Gale NW, Aldrich TH, Maisonpierre PC, Lhotak V, Pawson T, et al. Ligands for EPH-related receptor tyrosine kinases that require membrane attachment or clustering

[72] Holen HL, Zernichow L, Fjelland KE, Evenroed IM, Tveit H, Aasheim HC. Ephrin-B3 binds specifically to B lymphocytes in blood and induces migration. Scandinavian

gene polymorphism with asthma. Chest. 2009;135(5):1173-1180

germinal centers. Molecular Systems Biology. 2010;6:377

184 Gene Expression and Regulation in Mammalian Cells - Transcription From General Aspects

British Journal of Dermatology. 2009;160(3):633-641

glioma. Neuro-Oncology. 2011;13(11):1163-1170

Cancer Cell International. 2017;17:21

for activity. Science. 1994;266(5186):816-819

Journal of Immunology. 2011;74(2):144-154

nary Medicine. 2011;11:17

34(2):227-233

Clinical Cancer Research: An Official Journal of the American Association for Cancer Research. 2013;19(6):1577-1586

[100] Thornton AM, Korty PE, Tran DQ, Wohlfert EA, Murray PE, Belkaid Y, et al. Expression of Helios, an Ikaros transcription factor family member, differentiates thymic-derived from peripherally induced Foxp3+ T regulatory cells. Journal of Immunology. 2010;184(7):

Gene Expression during the Activation of Human B Cells http://dx.doi.org/10.5772/intechopen.71863 187

[101] Santos-Cortez RL, Lee K, Giese AP, Ansar M, Amin-Ud-Din M, Rehn K, et al. Adenylate cyclase 1 (ADCY1) mutations cause recessive hearing impairment in humans and defects in hair cell function and hearing in zebrafish. Human Molecular Genetics. 2014;23(12):3289-3298

[102] Gawad C, Koh W, Quake SR. Single-cell genome sequencing: Current state of the science.

[103] Bertsias GK, Salmon JE, Boumpas DT. Therapeutic opportunities in systemic lupus erythematosus: State of the art and prospects for the new decade. Annals of the Rheu-

[104] Sanz I, Lee FEB. Cells as therapeutic targets in SLE. Nature Reviews Rheumatology.

[105] Inoue M, Yamada J, Aomatsu-Kikuchi E, Satoh K, Kondo H, Ishisaki A, et al. SCRG1 suppresses LPS-induced CCL22 production through ERK1/2 activation in mouse mac-

[106] Oeckinghaus A, Hayden MS, Ghosh S. Crosstalk in NF-kappaB signaling pathways.

[107] Das UN, Rao AA. Gene expression profile in obesity and type 2 diabetes mellitus. Lipids

[108] Suhasini M, Pilz RB. Transcriptional elongation of c-myb is regulated by NF-kappaB

[110] Kondoh K, Nishida E. Regulation of MAP kinases by MAP kinase phosphatases.

[111] Dunkelberger JR, Song WC. Complement and its role in innate and adaptive immune

[112] Li JZ, Bunney BG, Meng F, Hagenauer MH, Walsh DM, Vawter MP, et al. Circadian patterns of gene expression in the human brain and disruption in major depressive disorder. Proceedings of the National Academy of Sciences of the United States of

[113] Pone EJ, Zhang J, Mai T, White CA, Li G, Sakakura JK, et al. BCR-signalling synergizes with TLR-signalling for induction of AID and immunoglobulin class-switching through

[114] Coulthard MG, Morgan M, Woodruff TM, Arumugam TV, Taylor SM, Carpenter TC, et al. Eph/Ephrin signaling in injury and inflammation. The American Journal of Pathol-

the non-canonical NF-kappaB pathway. Nature Communications. 2012;3:767

[109] Kawai T, Akira S. TLR signaling. Cell Death and Differentiation. 2006;13(5):816-825

rophage Raw264.7 cells. Molecular Medicine Reports. 2017;15(6):4069-4076

Nature Reviews Genetics. 2016;17(3):175-188

matic Diseases. 2010;69(9):1603-1611

Nature Immunology. 2011;12(8):695-708

(p50/RelB). Oncogene. 1999;18(51):7360-7369

responses. Cell Research. 2010;20(1):34-50

America. 2013;110(24):9950-9955

ogy. 2012;181(5):1493-1503

Biochimica et Biophysica Acta. 2007;1773(8):1227-1237

in Health and Disease. 2007;6:35

3433-3441

2010;6(6):326-337

[100] Thornton AM, Korty PE, Tran DQ, Wohlfert EA, Murray PE, Belkaid Y, et al. Expression of Helios, an Ikaros transcription factor family member, differentiates thymic-derived from peripherally induced Foxp3+ T regulatory cells. Journal of Immunology. 2010;184(7): 3433-3441

Clinical Cancer Research: An Official Journal of the American Association for Cancer

[87] Glotzer M. The molecular requirements for cytokinesis. Science. 2005;307(5716):1735-1739 [88] Gruneberg U, Neef R, Li X, Chan EH, Chalamalasetty RB, Nigg EA, et al. KIF14 and citron kinase act together to promote efficient cytokinesis. The Journal of Cell Biology.

[89] Chattopadhyay S, Bielinsky AK. Human Mcm10 regulates the catalytic subunit of DNA polymerase-alpha and prevents DNA damage during replication. Molecular Biology of

[90] Xu X, Rochette PJ, Feyissa EA, TV S, Liu Y. MCM10 mediates RECQ4 association with MCM2–7 helicase complex during DNA replication. The EMBO Journal. 2009;28(19):

[91] Kliszczak M, Sedlackova H, Pitchai GP, Streicher WW, Krejci L, Hickson ID. Interaction of RECQ4 and MCM10 is important for efficient DNA replication origin firing in human

[92] Strzalka W, Ziemienowicz A. Proliferating cell nuclear antigen (PCNA): A key factor in DNA replication and cell cycle regulation. Annals of Botany. 2011;107(7):1127-1140 [93] Nakano T, Kamei R, Fujimura T, Takaoka Y, Hori A, Lai CY, et al. Impact of histone H1 on the progression of allergic rhinitis and its suppression by neutralizing antibody in

[94] Kohno M, Hasegawa H, Inoue A, Muraoka M, Miyazaki T, Oka K, et al. Identification of N-arachidonylglycine as the endogenous ligand for orphan G-protein-coupled receptor GPR18. Biochemical and Biophysical Research Communications. 2006;347(3):827-832

[95] Flegel C, Vogel F, Hofreuter A, Wojcik S, Schoeder C, Kiec-Kononowicz K, et al. Characterization of non-olfactory GPCRs in human sperm with a focus on GPR18. Scientific

[96] Shahbazi J, Lock R, Liu T. Tumor protein 53-induced nuclear protein 1 enhances p53

[97] Seillier M, Peuget S, Gayet O, Gauthier C, N'Guessan P, Monte M, et al. TP53INP1, a tumor suppressor, interacts with LC3 and ATG8-family proteins through the LC3 interacting region (LIR) and promotes autophagy-dependent cell death. Cell Death and

[98] Del Nery E, Miserey-Lenkei S, Falguieres T, Nizak C, Johannes L, Perez F, et al. Rab6A and Rab6A' GTPases play non-overlapping roles in membrane trafficking. Traffic. 2006;

[99] Opdam FJ, Echard A, Croes HJ, van den Hurk JA, van de Vorstenbosch RA, Ginsel LA, et al. The small GTPase Rab6B, a novel Rab6 subfamily member, is cell-type specifically expressed and localised to the Golgi apparatus. Journal of Cell Science. 2000;113(Pt 15):

function and represses tumorigenesis. Frontiers in Genetics. 2013;4:80

Research. 2013;19(6):1577-1586

186 Gene Expression and Regulation in Mammalian Cells - Transcription From General Aspects

the Cell. 2007;18(10):4085-4095

cells. Oncotarget. 2015;6(38):40464-40479

mice. PLoS One. 2016;11(4):e0153630

Differentiation. 2012;19(9):1525-1535

Reports. 2016;6:32255

7(4):394-407

2725-2735

2006;172(3):363-372

3005-3014

[115] Lee SJ, Park SS, Cho YH, Park K, Kim EJ, Jung KH, et al. Activation of matrix metalloproteinase-9 by TNF-alpha in human urinary bladder cancer HT1376 cells: The role of MAP kinase signaling pathways. Oncology Reports. 2008;19(4):1007-1013

[129] Millan-Arino L, Islam AB, Izquierdo-Bouldstridge A, Mayor R, Terme JM, Luque N, et al. Mapping of six somatic linker histone H1 variants in human breast cancer cells

Gene Expression during the Activation of Human B Cells http://dx.doi.org/10.5772/intechopen.71863 189

uncovers specific features of H1.2. Nucleic Acids Research. 2014;42(7):4474-4493 [130] Wen L, Yang Z, Cui W, Li MD. Crucial roles of the CHRNB3-CHRNA6 gene cluster on chromosome 8 in nicotine dependence: Update and subjects for future research. Trans-

[131] Yin H, Chu A, Li W, Wang B, Shelton F, Otero F, et al. Lipid G protein-coupled receptor ligand identification using beta-arrestin PathHunter assay. The Journal of Biological

[132] Perwitasari O, Cho H, Diamond MS, Gale M Jr. Inhibitor of kappaB kinase epsilon (IKK (epsilon)), STAT1, and IFIT2 proteins define novel innate immune effector pathway against West Nile virus infection. The Journal of Biological Chemistry. 2011;286(52):44412-44423

[133] Acquati F, Monti L, Lualdi M, Fabbri M, Sacco MG, Gribaldo L, et al. Molecular signature induced by RNASET2, a tumor antagonizing gene, in ovarian cancer cells.

[134] Schlager MA, Kapitein LC, Grigoriev I, Burzynski GM, Wulf PS, Keijzer N, et al. Pericentrosomal targeting of Rab6 secretory vesicles by Bicaudal-D-related protein 1

[135] Zanger UM, Schwab M. Cytochrome P450 enzymes in drug metabolism: Regulation of gene expression, enzyme activities, and impact of genetic variation. Pharmacology &

[136] Ward-Kavanagh LK, Lin WW, Sedy JR, Ware CF. The TNF receptor superfamily in co-

[137] Li MM, Emerman M. Polymorphism in human APOBEC3H affects a phenotype dominant for subcellular localization and antiviral activity. Journal of Virology. 2011;85(16):

[138] Steidl C, Gascoyne RD. The molecular pathogenesis of primary mediastinal large B-cell

[139] Elliot DJ, Suharjono LBC, Gillam EM, Birkett DJ, Gross AS, et al. Identification of the human cytochromes P450 catalysing the rate-limiting pathways of gliclazide elimina-

tion. British Journal of Clinical Pharmacology. 2007;64(4):450-457

stimulating and co-inhibitory responses. Immunity. 2016;44(5):1005-1019

(BICDR-1) regulates neuritogenesis. The EMBO Journal. 2010;29(10):1637-1651

lational Psychiatry. 2016;6(6):e843

Chemistry. 2009;284(18):12328-12338

Oncotarget. 2011;2(6):477-484

Therapeutics. 2013;138(1):103-141

lymphoma. Blood. 2011;118(10):2659-2669

8197-8207

[129] Millan-Arino L, Islam AB, Izquierdo-Bouldstridge A, Mayor R, Terme JM, Luque N, et al. Mapping of six somatic linker histone H1 variants in human breast cancer cells uncovers specific features of H1.2. Nucleic Acids Research. 2014;42(7):4474-4493

[115] Lee SJ, Park SS, Cho YH, Park K, Kim EJ, Jung KH, et al. Activation of matrix metalloproteinase-9 by TNF-alpha in human urinary bladder cancer HT1376 cells: The role of MAP kinase signaling pathways. Oncology Reports. 2008;19(4):1007-1013 [116] Mastrototaro L, Tietjen U, Sponder G, Vormann J, Aschenbach JR, Kolisek M. Insulin modulates the Na+/Mg2+ exchanger SLC41A1 and influences Mg2+ efflux from intracellular stores in transgenic HEK293 cells. The Journal of Nutrition. 2015;145(11):2440-2447

188 Gene Expression and Regulation in Mammalian Cells - Transcription From General Aspects

[117] Miller AJ, Levy C, Davis IJ, Razin E, Fisher DE. Sumoylation of MITF and its related family members TFE3 and TFEB. The Journal of Biological Chemistry. 2005;280(1):146-155

[118] Pecina-Slaus N. Wnt signal transduction pathway and apoptosis: A review. Cancer Cell

[119] Yang SH, Chang SY, Yin L, Tu Y, Hu Y, Yoshinaga Y, et al. An absence of both lamin B1 and lamin B2 in keratinocytes has no effect on cell proliferation or the development of

[120] Shi YF, Fong CC, Zhang Q, Cheung PY, Tzang CH, RS W, et al. Hypoxia induces the activation of human hepatic stellate cells LX-2 through TGF-beta signaling pathway.

[121] Du J, Johnson LM, Jacobsen SE, Patel DJDNA. Methylation pathways and their crosstalk with histone methylation. Nature Reviews Molecular Cell Biology. 2015;16(9):519-532

[122] Khanna KK, Jackson SP. DNA double-strand breaks: Signaling, repair and the cancer

[123] Tseliou M, Al-Qahtani A, Alarifi S, Alkahtani SH, Stournaras C, Sourvinos G. The role of RhoA, RhoB and RhoC GTPases in cell morphology, proliferation and migration in human cytomegalovirus (HCMV) infected glioblastoma cells. Cellular Physiology and Biochemistry: International Journal of Experimental Cellular Physiology, Biochemistry,

[124] Katsha A, Belkhiri A, Goff L, El-Rifai W. Aurora kinase A in gastrointestinal cancers:

[125] Moldovan GL, Pfander B, Jentsch S. PCNA the maestro of the replication fork. Cell.

[126] Huen MS, Chen J. The DNA damage response pathways: At the crossroad of protein

[127] Mjelle R, Hegre SA, Aas PA, Slupphaug G, Drablos F, Saetrom P, et al. Cell cycle regulation of human DNA repair and chromatin remodeling genes. DNA Repair.

[128] Shi GX, Harrison K, Han SB, Moratz C, Kehrl JH. Toll-like receptor signaling alters the expression of regulator of G protein signaling proteins in dendritic cells: Implications for G protein-coupled receptor signaling. Journal of Immunology. 2004;172(9):5175-5184

skin and hair. Human Molecular Genetics. 2011;20(18):3537-3544

International. 2010;10:22

FEBS Letters. 2007;581(2):203-210

and Pharmacology. 2016;38(1):94-109

2007;129(4):665-679

2015;30:53-67

Time to target. Molecular Cancer. 2015;14:106

modifications. Cell Research. 2008;18(1):8-16

connection. Nature Genetics. 2001;27(3):247-254

**Chapter 10**

**Provisional chapter**

**The Interplay between Transcription Factors and**

**The Interplay between Transcription Factors and**

DOI: 10.5772/intechopen.73027

Functionally polarized CD4 T helper (Th) cells, such as Th1, Th2, and Th17 cells, are essential for the regulation of acquired immunity. Differentiation of naïve CD4 T cells into Th2 cells is characterized by chromatin remodeling and the induced expression of a set of Th2-specific genes, which include Th2 cytokine genes. In the first stage of this differentiation, a Th2-skewing cytokine environment, especially IL-4, induces STAT6 activation. Activated STAT6 increases the expression of GATA3, a master regulator of Th2 cell differentiation, via direct binding to the *Gata3* gene locus. This transcriptional induction of *Gata3* mRNA during Th2 cell differentiation is accompanied by dynamic changes in the binding patterns of two epigenetic modification proteins such as Polycomb and Trithorax complexes. Consequently, expressed GATA3 epigenetically modifies and upregulates Th2-specific genes to establish Th2 cell identity. This identity is maintained by high-level expression of the *Gata*3 gene controlled by Menin, which is a member of the Trithorax proteins, after cycles of cultivation *in vitro* and a long-term resting state *in vivo*.

Thus, the Menin-GATA3 axis handles the Th2-specific gene regulatory network.

© 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution,

© 2018 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

and reproduction in any medium, provided the original work is properly cited.

Naïve CD4-positive (CD4+) T cells can differentiate into several effector T cell subsets, mainly known as Th1, Th2, and Th17 cells [1]. Th1 cells perform the crucial function of protecting against viruses and intracellular pathogens. Th17 cells similarly work against extracellular bacteria or fungi. Th2 cells are required for the removal of extracellular parasites. Each effector subset exerts its protective functions through the secretion of unique cytokines. Th1 cells mainly produce IFN-γ, which activates macrophages and CD8 T cells. Th17 cells secrete IL-17A, which

**Epigenetic Modifications in Th2 Cells**

Atsushi Onodera, Kota Kokubo and Toshinori Nakayama

**Epigenetic Modifications in Th2 Cells**

Atsushi Onodera, Kota Kokubo and

http://dx.doi.org/10.5772/intechopen.73027

Additional information is available at the end of the chapter

**Keywords:** Th2, GATA3, STAT6, Menin

Additional information is available at the end of the chapter

Toshinori Nakayama

**Abstract**

**1. Introduction**

#### **The Interplay between Transcription Factors and Epigenetic Modifications in Th2 Cells The Interplay between Transcription Factors and Epigenetic Modifications in Th2 Cells**

DOI: 10.5772/intechopen.73027

Atsushi Onodera, Kota Kokubo and Toshinori Nakayama Atsushi Onodera, Kota Kokubo and Toshinori Nakayama Additional information is available at the end of the chapter

Additional information is available at the end of the chapter

http://dx.doi.org/10.5772/intechopen.73027

#### **Abstract**

Functionally polarized CD4 T helper (Th) cells, such as Th1, Th2, and Th17 cells, are essential for the regulation of acquired immunity. Differentiation of naïve CD4 T cells into Th2 cells is characterized by chromatin remodeling and the induced expression of a set of Th2-specific genes, which include Th2 cytokine genes. In the first stage of this differentiation, a Th2-skewing cytokine environment, especially IL-4, induces STAT6 activation. Activated STAT6 increases the expression of GATA3, a master regulator of Th2 cell differentiation, via direct binding to the *Gata3* gene locus. This transcriptional induction of *Gata3* mRNA during Th2 cell differentiation is accompanied by dynamic changes in the binding patterns of two epigenetic modification proteins such as Polycomb and Trithorax complexes. Consequently, expressed GATA3 epigenetically modifies and upregulates Th2-specific genes to establish Th2 cell identity. This identity is maintained by high-level expression of the *Gata*3 gene controlled by Menin, which is a member of the Trithorax proteins, after cycles of cultivation *in vitro* and a long-term resting state *in vivo*. Thus, the Menin-GATA3 axis handles the Th2-specific gene regulatory network.

**Keywords:** Th2, GATA3, STAT6, Menin

## **1. Introduction**

Naïve CD4-positive (CD4+) T cells can differentiate into several effector T cell subsets, mainly known as Th1, Th2, and Th17 cells [1]. Th1 cells perform the crucial function of protecting against viruses and intracellular pathogens. Th17 cells similarly work against extracellular bacteria or fungi. Th2 cells are required for the removal of extracellular parasites. Each effector subset exerts its protective functions through the secretion of unique cytokines. Th1 cells mainly produce IFN-γ, which activates macrophages and CD8 T cells. Th17 cells secrete IL-17A, which

© 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. © 2018 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

propagates cascades of events that lead to neutrophil recruitment, inflammation, and host defense [2]. Th2 cells activate B cells to induce immunoglobulin class switching through IL-4, and enhance mucus production from epithelial cells by IL-13. In addition, Th2 cells recruit eosinophils to induce an inflammatory response through IL-5. However, the responses caused by these subsets are sometimes excessive and result in immunological diseases. For example, an excess amount of Th2 cytokines is known to induce allergic disease, such as asthma [3].

reported that STAT6 also exerts an inhibitory function by occupying overlapping binding sites of other transcription factors and blocking their binding [16, 17]. It is now well known that STATmediated repression is important for the lineage commitment of Th subsets [18]. For example, STAT6 binds to the genomic loci of Th1-associated genes and inhibits their expression, and STAT4,

The Interplay between Transcription Factors and Epigenetic Modifications in Th2 Cells

http://dx.doi.org/10.5772/intechopen.73027

193

It has been proposed that the IL-4/STAT6 cascade is necessary for the Th2 phenotype. This fact is also demonstrated by a series of knockout studies. In these studies, IL-4 deficient mice showed impaired Th2 responses, attributed to a reduced Th2 effector cytokine production, loss of IgE class switching, and reduced eosinophilia upon infection with *Nippostrongylus brasiliensis* [20]. A similar but more significant phenotype is observed in STAT6 knockout mice. In addition, STAT6 appears to be highly specific to Th2 functions, as the phenotype of STAT6 deficient mice is largely related to the loss of the Th2 cell function, and deficient mice show normal development with ordinary numbers of T cells [21, 22]. Other STAT signaling cascades are also involved in Th2 polarization. STAT5A and STAT3, which are activated by IL-2 [23] and IL-6 [24], respectively, are also reported to induce the Th2 phenotype. However, STAT5 and STAT3 are activated not only in Th2 but also in other CD4+ T cell subsets. Therefore, only

The GATA family proteins (GATA1–6) are conserved transcription factors that contain one or two C2-C2-type zinc-finger motif that recognize the consensus DNA sequence WGATAR [25–27]. Each member of the GATA family has different expression patterns in the body and can be grouped into hematopoietic factors (GATA1–3) and endodermal factors (GATA4–6). Among hematopoietic cells, immune cells, particularly developing and mature T cells, natural killer (NK) cells, and CD1-restricted NKT cells, mainly express GATA-binding protein 3 (GATA3) [6, 28, 29]. Mature mast cells express GATA1 and GATA2 but not GATA3 [30]. Outside of the immune system, GATA3 is also expressed in many embryonic and adult tissues, including the adrenal glands, kidneys, central nervous system, inner ear, hair follicles and skin, and breast tissue [27].

In the immune system, GATA3 is predominantly expressed in T lymphocytes and is essential for the development of CD4 single-positive (SP) cells in the thymus [31–33]. GATA3 exerts an important function at the β-selection checkpoint, which is involved in the CD4 versus CD8 lineage choice in the thymus [34]. It is continuously expressed in peripheral naïve CD4 T cells at a basal level, where the activation of STAT6 induced by the IL-4/IL-4 receptor signaling pathway upregulates *Gata3* mRNA expression during Th2 cell differentiation [35]. GATA3 is thought to be necessary as the master regulator of Th2 differentiation [6, 7], since enforced GATA3 expression induces Th2 differentiation even when the cells are cultured under Th1 skewing conditions [35]. Enforced expression of GATA3 has also been reported to endogenously upregulate GATA3 expression [36]. In addition, the amount of GATA3 protein in Th2 cells is regulated by various posttranscriptional mechanisms [37–39]. Furthermore, high-level expression of GATA3 is essential for the production of large amounts of Th2 cytokines in established Th2 cells [11, 40–42]. The detailed mechanisms underlying the GATA3-dependent

a key transcription factor of Th1, acts on Th2-associated genes in a similar way [19].

**2.2. GATA3 plays roles in various tissues as well as the immune system**

STAT6 exclusively promotes Th2 differentiation.

regulation of its target genes are described in Section 5.

Each subset-specific cytokine enhances differentiation toward the corresponding Th subset, and environmental cytokines decide the differentiation fate of CD4 T cells. For example, IL-12 induced STAT4 activation in Th1 cells and IL-4-induced STAT6 activation in Th2 cells are essential for their respective differentiation [4, 5]. These STAT signals are commonly used for CD4 T cell differentiation into each subset and induce the upregulation of master transcription factors, T-bet in Th1 and GATA3 in Th2 [6, 7]. The master transcription factors directly bind to DNA and regulate the expression of each subset-specific gene, causing epigenetic modification of the DNA, which stabilizes the differentiation program. Due to this epigenetic modification, fully differentiated effector T cells are rarely converted to other Th subsets and are able to maintain their identity during the transition from effector to memory cells.

The Th2 master transcription factor GATA3 collaborates with the epigenetic regulator Menin to induce and stabilize the complex gene regulatory network. Th2-specific genes, which have been identified by gene expression profiling [8, 9], participate in this regulatory network and are controlled by neither, either or both GATA3 and Menin [10]. In fact, GATA3 or Menin deletion results in the loss of Th2 identity [10, 11]. Clarifying the interplay between the transcription factors and epigenetic modifiers is required to comprehend the Th2 cell biology and to identify new therapeutic targets for Th2-mediated immunological diseases [3].

## **2. STAT6 and GATA3: important transcription factors for Th2 cells**

#### **2.1. STAT6 is activated by IL-4 signaling**

The most essential pathway promoting the Th2 fate is the IL-4 signaling cascade, followed by activating the transcription factor STAT6 [12–14]. When IL-4 is recognized by its receptor (type-I IL-4R), which consists of IL-4 receptor alpha chain (IL-4Rα) and a common gamma chain (γc), IL-4 can transmit a signal into a cell. Binding of IL-4 induces dimerization of IL-4Rα and γc, resulting in the phosphorylation of tyrosine residues within the intracellular portion of IL-4Rα by Janus Kinases. This phosphorylated intracellular portion of IL-4Rα recruits and phosphorylates signal transducer and activator of transcription (STAT)6, which then forms a dimer and translocates into the nucleus where the dimerized STAT6 regulates the expression of IL-4 target genes. STAT6 recognizes the DNA sequence TTCNNNNGAA, whereas other STAT family proteins prefer the DNA sequence TTCNNNGAA [15].

Like other STAT proteins, a major role of STAT6 is to activate the expression of its target genes, which is how it received its name ("signal transducer and activator of transcription"). The bestknown target gene of STAT6 is the *Gata3* gene, and the detailed mechanisms underlying the STAT6 dependent regulation of the *Gata3* gene are described in Section 4. However, some studies have reported that STAT6 also exerts an inhibitory function by occupying overlapping binding sites of other transcription factors and blocking their binding [16, 17]. It is now well known that STATmediated repression is important for the lineage commitment of Th subsets [18]. For example, STAT6 binds to the genomic loci of Th1-associated genes and inhibits their expression, and STAT4, a key transcription factor of Th1, acts on Th2-associated genes in a similar way [19].

propagates cascades of events that lead to neutrophil recruitment, inflammation, and host defense [2]. Th2 cells activate B cells to induce immunoglobulin class switching through IL-4, and enhance mucus production from epithelial cells by IL-13. In addition, Th2 cells recruit eosinophils to induce an inflammatory response through IL-5. However, the responses caused by these subsets are sometimes excessive and result in immunological diseases. For example, an excess amount of Th2 cytokines is known to induce allergic disease, such as asthma [3].

192 Gene Expression and Regulation in Mammalian Cells - Transcription From General Aspects

Each subset-specific cytokine enhances differentiation toward the corresponding Th subset, and environmental cytokines decide the differentiation fate of CD4 T cells. For example, IL-12 induced STAT4 activation in Th1 cells and IL-4-induced STAT6 activation in Th2 cells are essential for their respective differentiation [4, 5]. These STAT signals are commonly used for CD4 T cell differentiation into each subset and induce the upregulation of master transcription factors, T-bet in Th1 and GATA3 in Th2 [6, 7]. The master transcription factors directly bind to DNA and regulate the expression of each subset-specific gene, causing epigenetic modification of the DNA, which stabilizes the differentiation program. Due to this epigenetic modification, fully differentiated effector T cells are rarely converted to other Th subsets and

are able to maintain their identity during the transition from effector to memory cells.

identify new therapeutic targets for Th2-mediated immunological diseases [3].

STAT family proteins prefer the DNA sequence TTCNNNGAA [15].

**2.1. STAT6 is activated by IL-4 signaling**

**2. STAT6 and GATA3: important transcription factors for Th2 cells**

The most essential pathway promoting the Th2 fate is the IL-4 signaling cascade, followed by activating the transcription factor STAT6 [12–14]. When IL-4 is recognized by its receptor (type-I IL-4R), which consists of IL-4 receptor alpha chain (IL-4Rα) and a common gamma chain (γc), IL-4 can transmit a signal into a cell. Binding of IL-4 induces dimerization of IL-4Rα and γc, resulting in the phosphorylation of tyrosine residues within the intracellular portion of IL-4Rα by Janus Kinases. This phosphorylated intracellular portion of IL-4Rα recruits and phosphorylates signal transducer and activator of transcription (STAT)6, which then forms a dimer and translocates into the nucleus where the dimerized STAT6 regulates the expression of IL-4 target genes. STAT6 recognizes the DNA sequence TTCNNNNGAA, whereas other

Like other STAT proteins, a major role of STAT6 is to activate the expression of its target genes, which is how it received its name ("signal transducer and activator of transcription"). The bestknown target gene of STAT6 is the *Gata3* gene, and the detailed mechanisms underlying the STAT6 dependent regulation of the *Gata3* gene are described in Section 4. However, some studies have

The Th2 master transcription factor GATA3 collaborates with the epigenetic regulator Menin to induce and stabilize the complex gene regulatory network. Th2-specific genes, which have been identified by gene expression profiling [8, 9], participate in this regulatory network and are controlled by neither, either or both GATA3 and Menin [10]. In fact, GATA3 or Menin deletion results in the loss of Th2 identity [10, 11]. Clarifying the interplay between the transcription factors and epigenetic modifiers is required to comprehend the Th2 cell biology and to It has been proposed that the IL-4/STAT6 cascade is necessary for the Th2 phenotype. This fact is also demonstrated by a series of knockout studies. In these studies, IL-4 deficient mice showed impaired Th2 responses, attributed to a reduced Th2 effector cytokine production, loss of IgE class switching, and reduced eosinophilia upon infection with *Nippostrongylus brasiliensis* [20]. A similar but more significant phenotype is observed in STAT6 knockout mice. In addition, STAT6 appears to be highly specific to Th2 functions, as the phenotype of STAT6 deficient mice is largely related to the loss of the Th2 cell function, and deficient mice show normal development with ordinary numbers of T cells [21, 22]. Other STAT signaling cascades are also involved in Th2 polarization. STAT5A and STAT3, which are activated by IL-2 [23] and IL-6 [24], respectively, are also reported to induce the Th2 phenotype. However, STAT5 and STAT3 are activated not only in Th2 but also in other CD4+ T cell subsets. Therefore, only STAT6 exclusively promotes Th2 differentiation.

#### **2.2. GATA3 plays roles in various tissues as well as the immune system**

The GATA family proteins (GATA1–6) are conserved transcription factors that contain one or two C2-C2-type zinc-finger motif that recognize the consensus DNA sequence WGATAR [25–27]. Each member of the GATA family has different expression patterns in the body and can be grouped into hematopoietic factors (GATA1–3) and endodermal factors (GATA4–6). Among hematopoietic cells, immune cells, particularly developing and mature T cells, natural killer (NK) cells, and CD1-restricted NKT cells, mainly express GATA-binding protein 3 (GATA3) [6, 28, 29]. Mature mast cells express GATA1 and GATA2 but not GATA3 [30]. Outside of the immune system, GATA3 is also expressed in many embryonic and adult tissues, including the adrenal glands, kidneys, central nervous system, inner ear, hair follicles and skin, and breast tissue [27].

In the immune system, GATA3 is predominantly expressed in T lymphocytes and is essential for the development of CD4 single-positive (SP) cells in the thymus [31–33]. GATA3 exerts an important function at the β-selection checkpoint, which is involved in the CD4 versus CD8 lineage choice in the thymus [34]. It is continuously expressed in peripheral naïve CD4 T cells at a basal level, where the activation of STAT6 induced by the IL-4/IL-4 receptor signaling pathway upregulates *Gata3* mRNA expression during Th2 cell differentiation [35]. GATA3 is thought to be necessary as the master regulator of Th2 differentiation [6, 7], since enforced GATA3 expression induces Th2 differentiation even when the cells are cultured under Th1 skewing conditions [35]. Enforced expression of GATA3 has also been reported to endogenously upregulate GATA3 expression [36]. In addition, the amount of GATA3 protein in Th2 cells is regulated by various posttranscriptional mechanisms [37–39]. Furthermore, high-level expression of GATA3 is essential for the production of large amounts of Th2 cytokines in established Th2 cells [11, 40–42]. The detailed mechanisms underlying the GATA3-dependent regulation of its target genes are described in Section 5.

## **3. Polycomb and Trithorax proteins: fundamental epigenetic regulators for cell differentiation**

#### **3.1. Polycomb and Trithorax proteins epigenetically modify chromatin in a different way**

that these proteins are associated with more than simple gene activation [53]. TrxG proteins have more diverse binding molecules than PcG proteins with which they form complexes.

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195

Although many studies have been performed on the nature of PcG proteins and TrxG proteins individually, few have successfully defined how transcriptional counter-regulation is organized by the PcG and TrxG complexes. One pioneering work demonstrated the dynamic transformations of histone modifications during T cell development [57]. In addition, in our previous study, we successfully analyzed how the global signature of PcG and TrxG co-occupied genes changed during the developmental process. This study showed that a binding pattern in which Ezh2 binds upstream and Menin binds downstream of the transcription start site was frequently found at highly expressed genes, and a binding pattern in which Ezh2 and Menin bind to opposite positions was frequently found at low-expressed genes in T lymphocytes. Interestingly, genes showing a binding pattern in which Ezh2 and Menin occupied the

**3.2. Spatial interplay between Polycomb and Trithorax complexes**

same position displayed greatly enhanced sensitivity to Ezh2 deletion [3, 58].

**gene locus**

**4. STAT6 induces dynamic changes in epigenetic states at the** *Gata3*

Epigenetic changes at the *Gata3* gene locus in T cells are essential for the acquisition and maintenance of the Th2 cell identity [3, 51, 59]. During Th2 cell differentiation, PcG and TrxG proteins dynamically change their binding patterns at the *Gata3* gene locus. In addition, these epigenetic changes result in GATA3 protein upregulation that consequently induces chromatin remodeling at the Th2 cytokine gene loci, including *Il4*, *Il5*, and *Il13* [51, 59]. The *Gata3* gene is known to have distal and proximal promoters. Both basal transcription in naïve CD4 T cells and induced transcription in differentiated Th2 cells are controlled by the proximal promoter [51, 60]. In naïve CD4 T cells, PcG complexes bind upstream and TrxG complexes bind downstream of the *Gata3* proximal promoter [51]. During Th2 cell differentiation, PcG proteins dissociate upstream of the *Gata3* proximal promoter, and the binding of TrxG proteins spreads into this region. Consequently, rapid alterations in the binding patterns of PcG and TrxG proteins are observed in the region between the *Gata3* distal and proximal promoters in this period. Histone modification patterns basically exhibit the same behavior; H3K27me3 levels are decreased at the upstream region of the *Gata3* proximal promoter, and H3K4me3 spreads into this region. In contrast, changes in DNA methylation pattern are only observed at exon 2, in which DNA is methylated in naïve CD4 T cells and demethylated in Th2 cells [61]. At present, the mechanism underlying this demethylation process remains unclear.

We identified two functional STAT6 binding sites within the intronic regions of the *Gata3* gene locus [51]. A chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq)

**4.1. The** *Gata3* **gene is epigenetically regulated during Th2 cell differentiation**

**4.2. STAT6 directly modifies epigenetic states at the** *Gata3* **gene locus**

Huge numbers of genes involved in epigenetic regulation have been identified. Many of them encode histone-modifying enzymatic proteins and their interaction partners. Among them, members of the Polycomb group (PcG) and Trithorax group (TrxG) complexes have been recognized as key epigenetic regulators [3, 43–46]. PcG and TrxG proteins were originally identified in *Drosophila*; however, they also play essential roles in controlling mammalian gene expression in various normal and tumor tissues. It has long been thought that PcG and TrxG proteins antagonize each other for turning target gene expression off or on, respectively. PcG proteins mediate gene silencing by controlling the repressive histone mark H3K27me3 (trimethylated histone H3 lysine 27), whereas TrxG proteins mediate gene activation by modifying the permissive histone mark H3K4me3. Both histone-modifying complexes are often found to regulate the same genes at different stages of development [47]. In addition, emerging evidence shows that PcG and TxrG proteins participate in complex regulatory mechanisms in mammalian tissues [48].

PcG complexes are classified into two canonical types such as Polycomb repressive complex 1 (PRC1) and PRC2. Both of them are involved in transcriptional repression. A sequential recruiting mechanism is proposed for the binding of PRC2 and PRC1 to genomic DNA. First, enhancer of zeste (EZH), the enzymatically active subunit of PRC2, methylates H3K27. Next, the PRC1 complex recognizes trimethylated H3K27, resulting in its co-localization with PRC2. In addition, the ring finger protein 1 (RING1), a subunit of PRC1, has a ubiquitin ligase activity for histone H2AK119 [49]. In CD4+ T cells, Ezh2 appeared to directly bind and facilitate the correct expression of the *Gata3* gene during differentiation into effector Th2 cells [50, 51]. In our previous study, Ezh2 bound much more strongly to transcription factor genes, including the *Gata3* gene, than to the cytokine or cytokine receptor genes. Genome-wide, in the genes encoding transcription factors, the Ezh2 binding levels appear to be higher in non-expressed genes than in expressed genes [52].

In contrast, mixed lineage leukemia (MLL) family proteins, which are major subunits of the TrxG complex, have H3K4 methyltransferase activity that induces a change in the chromatin structure to a form permissive for transcription. In mammals, six H3K4 methylases (MLL1–4, SET1A, and SET1B) have been discovered [53]. The H3K4 methylase complexes containing MLL1 or MLL2 are associated with a unique subunit named Menin (encoded by the *Men1* gene in mice). A mutation of *MEN1* has been found in patients with multiple endocrine neoplasia type 1 (MEN1) syndrome [54, 55]. Menin can act as a tumor suppressor and is required for TrxG complex binding to DNA [53]. Menin is also indicated to have essential roles in the immune system, as Menin has been shown to be important for the Th2 cell function both in mice and humans [51, 56]. The MLL3- or MLL4-containing complex associates with the H3K27 demethylase UTX (encoded by the *Kdm6a* gene in mice) and induces demethylation. H3K4 trimethylation appears to be mediated by these MLL-associated complexes in a gene-specific manner. The SET1A- or SET1B-containing complexes have the unique WD repeat-containing 82 (WDR82). TrxG proteins activate target gene expression and/or keep them active, indicating that these proteins are associated with more than simple gene activation [53]. TrxG proteins have more diverse binding molecules than PcG proteins with which they form complexes.

#### **3.2. Spatial interplay between Polycomb and Trithorax complexes**

**3. Polycomb and Trithorax proteins: fundamental epigenetic**

194 Gene Expression and Regulation in Mammalian Cells - Transcription From General Aspects

**3.1. Polycomb and Trithorax proteins epigenetically modify chromatin in a different**

Huge numbers of genes involved in epigenetic regulation have been identified. Many of them encode histone-modifying enzymatic proteins and their interaction partners. Among them, members of the Polycomb group (PcG) and Trithorax group (TrxG) complexes have been recognized as key epigenetic regulators [3, 43–46]. PcG and TrxG proteins were originally identified in *Drosophila*; however, they also play essential roles in controlling mammalian gene expression in various normal and tumor tissues. It has long been thought that PcG and TrxG proteins antagonize each other for turning target gene expression off or on, respectively. PcG proteins mediate gene silencing by controlling the repressive histone mark H3K27me3 (trimethylated histone H3 lysine 27), whereas TrxG proteins mediate gene activation by modifying the permissive histone mark H3K4me3. Both histone-modifying complexes are often found to regulate the same genes at different stages of development [47]. In addition, emerging evidence shows that PcG and TxrG proteins participate in complex regulatory mechanisms in mammalian tissues [48].

PcG complexes are classified into two canonical types such as Polycomb repressive complex 1 (PRC1) and PRC2. Both of them are involved in transcriptional repression. A sequential recruiting mechanism is proposed for the binding of PRC2 and PRC1 to genomic DNA. First, enhancer of zeste (EZH), the enzymatically active subunit of PRC2, methylates H3K27. Next, the PRC1 complex recognizes trimethylated H3K27, resulting in its co-localization with PRC2. In addition, the ring finger protein 1 (RING1), a subunit of PRC1, has a ubiquitin ligase activity for histone H2AK119 [49]. In CD4+ T cells, Ezh2 appeared to directly bind and facilitate the correct expression of the *Gata3* gene during differentiation into effector Th2 cells [50, 51]. In our previous study, Ezh2 bound much more strongly to transcription factor genes, including the *Gata3* gene, than to the cytokine or cytokine receptor genes. Genome-wide, in the genes encoding transcription factors, the Ezh2 binding levels appear to be higher in non-expressed genes than in expressed genes [52]. In contrast, mixed lineage leukemia (MLL) family proteins, which are major subunits of the TrxG complex, have H3K4 methyltransferase activity that induces a change in the chromatin structure to a form permissive for transcription. In mammals, six H3K4 methylases (MLL1–4, SET1A, and SET1B) have been discovered [53]. The H3K4 methylase complexes containing MLL1 or MLL2 are associated with a unique subunit named Menin (encoded by the *Men1* gene in mice). A mutation of *MEN1* has been found in patients with multiple endocrine neoplasia type 1 (MEN1) syndrome [54, 55]. Menin can act as a tumor suppressor and is required for TrxG complex binding to DNA [53]. Menin is also indicated to have essential roles in the immune system, as Menin has been shown to be important for the Th2 cell function both in mice and humans [51, 56]. The MLL3- or MLL4-containing complex associates with the H3K27 demethylase UTX (encoded by the *Kdm6a* gene in mice) and induces demethylation. H3K4 trimethylation appears to be mediated by these MLL-associated complexes in a gene-specific manner. The SET1A- or SET1B-containing complexes have the unique WD repeat-containing 82 (WDR82). TrxG proteins activate target gene expression and/or keep them active, indicating

**regulators for cell differentiation**

**way**

Although many studies have been performed on the nature of PcG proteins and TrxG proteins individually, few have successfully defined how transcriptional counter-regulation is organized by the PcG and TrxG complexes. One pioneering work demonstrated the dynamic transformations of histone modifications during T cell development [57]. In addition, in our previous study, we successfully analyzed how the global signature of PcG and TrxG co-occupied genes changed during the developmental process. This study showed that a binding pattern in which Ezh2 binds upstream and Menin binds downstream of the transcription start site was frequently found at highly expressed genes, and a binding pattern in which Ezh2 and Menin bind to opposite positions was frequently found at low-expressed genes in T lymphocytes. Interestingly, genes showing a binding pattern in which Ezh2 and Menin occupied the same position displayed greatly enhanced sensitivity to Ezh2 deletion [3, 58].

## **4. STAT6 induces dynamic changes in epigenetic states at the** *Gata3* **gene locus**

#### **4.1. The** *Gata3* **gene is epigenetically regulated during Th2 cell differentiation**

Epigenetic changes at the *Gata3* gene locus in T cells are essential for the acquisition and maintenance of the Th2 cell identity [3, 51, 59]. During Th2 cell differentiation, PcG and TrxG proteins dynamically change their binding patterns at the *Gata3* gene locus. In addition, these epigenetic changes result in GATA3 protein upregulation that consequently induces chromatin remodeling at the Th2 cytokine gene loci, including *Il4*, *Il5*, and *Il13* [51, 59]. The *Gata3* gene is known to have distal and proximal promoters. Both basal transcription in naïve CD4 T cells and induced transcription in differentiated Th2 cells are controlled by the proximal promoter [51, 60]. In naïve CD4 T cells, PcG complexes bind upstream and TrxG complexes bind downstream of the *Gata3* proximal promoter [51]. During Th2 cell differentiation, PcG proteins dissociate upstream of the *Gata3* proximal promoter, and the binding of TrxG proteins spreads into this region. Consequently, rapid alterations in the binding patterns of PcG and TrxG proteins are observed in the region between the *Gata3* distal and proximal promoters in this period. Histone modification patterns basically exhibit the same behavior; H3K27me3 levels are decreased at the upstream region of the *Gata3* proximal promoter, and H3K4me3 spreads into this region. In contrast, changes in DNA methylation pattern are only observed at exon 2, in which DNA is methylated in naïve CD4 T cells and demethylated in Th2 cells [61]. At present, the mechanism underlying this demethylation process remains unclear.

#### **4.2. STAT6 directly modifies epigenetic states at the** *Gata3* **gene locus**

We identified two functional STAT6 binding sites within the intronic regions of the *Gata3* gene locus [51]. A chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq) analysis also identified one STAT6 binding site at the same region [62]. In the absence of STAT6, displacement of PcG by TrxG is not observed. These results indicate that STAT6 directly binds to the *Gata3* gene locus and induces PcG/TrxG displacement, although the precise mechanism is still unclear. A study of human Th2 cells indicated that STAT6 binding was hardly detected at the *GATA3* gene locus, although *STAT6* knockdown was effective for reducing the *GATA3* expression [18]. Interestingly, our ChIP-seq analysis detected one GATA3 binding peak close to one of the STAT6 binding sites at the *Gata3* gene locus [8, 51] and one of the strong peaks on the assay for transposase-accessible chromatin sequencing (ATAC-seq) [63]. This GATA3 binding site may be important for cis-regulation via GATA3-dependent auto activation of the *Gata3* gene [36]. Although STAT6 induces TrxG spreading into the promoter region, the T cell-specific deletion of Menin, a component of the TrxG complex, does not affect Th2 cell differentiation. This suggests that the induction of high-level expression of *Gata3* (i.e. the acquisition of the Th2 cell identity) is dependent on STAT6 and not the Menin/TrxG complex [51]. However, the maintenance of the *Gata3* expression is dependent on the Menin/TrxG complex and independent of IL-4 and STAT6 in Th2 cells. A similar molecular mechanism was found to underlie the *Gata3* expression *in vivo* [10, 64]. In human memory Th2 cells, MLL and Menin form a core transcriptional complex and regulate the *GATA3* expression [65]. Therefore, TrxG proteins represent an essential mechanism underlying transcriptional maintenance in the memory Th2 cell response [3].

IL-13 in Th2 cells, and GATA3 has been proposed to regulate chromatin remodeling at these genes. Notably, the H3K9 acetylation levels are higher around the GATA3 binding sites at the Th2 cytokine gene loci than the regions without GATA3 binding [8]. However, genome-wide surveys on GATA3 binding and histone modifications suggest that GATA3 binding do not perfectly coincide with changes in permissive histone modifications, which correlate highly with the states of transcription [62, 69]. In fact, some studies suggest that GATA3 acts not only as an activator but also as a repressor in both Th1 and Th2 cells [8]. Although GATA3 is recognized as a master regulator of Th2 cell differentiation, the transcription of many Th2-specific genes is not regulated

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by GATA3 itself; therefore, GATA3 is not the only essential factor for Th2 differentiation.

It has been reported that GATA3 interacts with some regulatory elements at Th2 cytokine gene loci, including conserved non-coding sequence (CNS)-1, HSVa, the conserved GATA response element (CGRE), and HSII in intron 2 of the *Il4* gene [12, 68, 70–74]. CNS-1 is located at the intergenic region between the *Il4* and *Il13* genes and was originally described as Th2 specific HS sites (HSS1 and HSS2) [75, 76]. To characterize the function of CNS-1, mice lacking this genomic region was generated [77]. Genetic deletion of the CNS-1 region resulted in a reduction of Th2 cells producing IL-4, IL-5, and IL-13. In this mutant mouse, IL-4 production *in vivo* was also abrogated [77]. However, CNS-1-deficieny had no effect on IL-4 production in bone marrow-derived mast cells [78]. This is consistent with the observation of no HS sites in CNS-1 of mast cells. Although an electrophoresis mobility shift assay showed that GATA3 binds to HSS2 *in vitro* [70, 71], two independent genome-wide GATA3 ChIP-seq data analyses failed to detect significant GATA3 binding peak in the CNS-1 region (**Figure 1**) [8, 79].

**Figure 1.** GATA3-dependent epigenetic and transcriptional regulation in the Th2 cytokine gene loci. Epigenetic permissive histone marks (H3K9 acetylation and H3K4 tri-methylation) in the Th2 cytokine loci are shown in Th1 and Th2 cells (GSE28292) using the IGV genome browser (http://www.broadinstitute.org/igv/). GATA3 ChIP-seq data with statistically significant peaks (asterisks) are also shown in Th2 cells. DNA methylation data are shown in CD4+ naïve T, Th1, and Th2 cells (GSE25688). Data from an assay for transposase-accessible chromatin sequencing (ATAC-Seq), which

identifies opened chromatin regions, were obtained for lung Th2 cells (GSE77695).

**5.2. Interaction between GATA3 and regulatory elements**

#### **4.3. PRC2 components prevent hyperactivation of the** *Gata3* **gene**

In contrast to TrxG proteins, PcG proteins are proposed to maintain their *Gata3* expression at an appropriate level in CD4 T cells [3]. T cell-specific deletion of Ezh2 enhances the sensitivity of IL-4 and results in *Gata3* upregulation and hyper-production of Th2 cytokines [50]. A ChIPseq analysis revealed that the Ezh2 binding levels were high at the *Gata3* gene locus but very low at the Th2 cytokine gene loci, indicating that Ezh2 controls the Th2 cytokine expression via direct binding to the *Gata3* gene locus. However, measurable levels of H3K27me3 were detected at the *Il4* and *Il13* genes loci, and direct regulation of H3K27me3 by Ezh2 at these genes has also been proposed as important for transcriptional silencing in Th1 cells [66]. In contrast, SUV39H1-dependent H3K9me3 has been found to maintain the silencing of Th1 cellrelated genes in Th2 cells [67].

## **5. GATA3-dependent epigenetic and transcriptional regulation in the Th2 cytokine gene loci**

#### **5.1. Chromatin remodeling induced by GATA3 at the Th2 cytokine gene loci**

Induction of changes in histone modifications has been reported at the *Il4*, *Il5*, and *Il13* gene loci (so-called the Th2 cytokine gene loci) during Th2 differentiation [12, 59, 68]. Particularly, histone H3K4 methylation and H3K9 acetylation play an important role in forming the open chromatin structure. Thus, the regions that acquire these histone modifications become accessible to transcription factors and are frequently associated with DNase I hypersensitive (HS) sites. Chromatin remodeling at the Th2 cytokine gene loci is necessary for the efficient expression of IL-4, IL-5, and IL-13 in Th2 cells, and GATA3 has been proposed to regulate chromatin remodeling at these genes. Notably, the H3K9 acetylation levels are higher around the GATA3 binding sites at the Th2 cytokine gene loci than the regions without GATA3 binding [8]. However, genome-wide surveys on GATA3 binding and histone modifications suggest that GATA3 binding do not perfectly coincide with changes in permissive histone modifications, which correlate highly with the states of transcription [62, 69]. In fact, some studies suggest that GATA3 acts not only as an activator but also as a repressor in both Th1 and Th2 cells [8]. Although GATA3 is recognized as a master regulator of Th2 cell differentiation, the transcription of many Th2-specific genes is not regulated by GATA3 itself; therefore, GATA3 is not the only essential factor for Th2 differentiation.

#### **5.2. Interaction between GATA3 and regulatory elements**

analysis also identified one STAT6 binding site at the same region [62]. In the absence of STAT6, displacement of PcG by TrxG is not observed. These results indicate that STAT6 directly binds to the *Gata3* gene locus and induces PcG/TrxG displacement, although the precise mechanism is still unclear. A study of human Th2 cells indicated that STAT6 binding was hardly detected at the *GATA3* gene locus, although *STAT6* knockdown was effective for reducing the *GATA3* expression [18]. Interestingly, our ChIP-seq analysis detected one GATA3 binding peak close to one of the STAT6 binding sites at the *Gata3* gene locus [8, 51] and one of the strong peaks on the assay for transposase-accessible chromatin sequencing (ATAC-seq) [63]. This GATA3 binding site may be important for cis-regulation via GATA3-dependent auto activation of the *Gata3* gene [36]. Although STAT6 induces TrxG spreading into the promoter region, the T cell-specific deletion of Menin, a component of the TrxG complex, does not affect Th2 cell differentiation. This suggests that the induction of high-level expression of *Gata3* (i.e. the acquisition of the Th2 cell identity) is dependent on STAT6 and not the Menin/TrxG complex [51]. However, the maintenance of the *Gata3* expression is dependent on the Menin/TrxG complex and independent of IL-4 and STAT6 in Th2 cells. A similar molecular mechanism was found to underlie the *Gata3* expression *in vivo* [10, 64]. In human memory Th2 cells, MLL and Menin form a core transcriptional complex and regulate the *GATA3* expression [65]. Therefore, TrxG proteins represent an essential mechanism underlying transcriptional maintenance in the memory Th2 cell response [3].

In contrast to TrxG proteins, PcG proteins are proposed to maintain their *Gata3* expression at an appropriate level in CD4 T cells [3]. T cell-specific deletion of Ezh2 enhances the sensitivity of IL-4 and results in *Gata3* upregulation and hyper-production of Th2 cytokines [50]. A ChIPseq analysis revealed that the Ezh2 binding levels were high at the *Gata3* gene locus but very low at the Th2 cytokine gene loci, indicating that Ezh2 controls the Th2 cytokine expression via direct binding to the *Gata3* gene locus. However, measurable levels of H3K27me3 were detected at the *Il4* and *Il13* genes loci, and direct regulation of H3K27me3 by Ezh2 at these genes has also been proposed as important for transcriptional silencing in Th1 cells [66]. In contrast, SUV39H1-dependent H3K9me3 has been found to maintain the silencing of Th1 cell-

**5. GATA3-dependent epigenetic and transcriptional regulation in**

Induction of changes in histone modifications has been reported at the *Il4*, *Il5*, and *Il13* gene loci (so-called the Th2 cytokine gene loci) during Th2 differentiation [12, 59, 68]. Particularly, histone H3K4 methylation and H3K9 acetylation play an important role in forming the open chromatin structure. Thus, the regions that acquire these histone modifications become accessible to transcription factors and are frequently associated with DNase I hypersensitive (HS) sites. Chromatin remodeling at the Th2 cytokine gene loci is necessary for the efficient expression of IL-4, IL-5, and

**5.1. Chromatin remodeling induced by GATA3 at the Th2 cytokine gene loci**

**4.3. PRC2 components prevent hyperactivation of the** *Gata3* **gene**

196 Gene Expression and Regulation in Mammalian Cells - Transcription From General Aspects

related genes in Th2 cells [67].

**the Th2 cytokine gene loci**

It has been reported that GATA3 interacts with some regulatory elements at Th2 cytokine gene loci, including conserved non-coding sequence (CNS)-1, HSVa, the conserved GATA response element (CGRE), and HSII in intron 2 of the *Il4* gene [12, 68, 70–74]. CNS-1 is located at the intergenic region between the *Il4* and *Il13* genes and was originally described as Th2 specific HS sites (HSS1 and HSS2) [75, 76]. To characterize the function of CNS-1, mice lacking this genomic region was generated [77]. Genetic deletion of the CNS-1 region resulted in a reduction of Th2 cells producing IL-4, IL-5, and IL-13. In this mutant mouse, IL-4 production *in vivo* was also abrogated [77]. However, CNS-1-deficieny had no effect on IL-4 production in bone marrow-derived mast cells [78]. This is consistent with the observation of no HS sites in CNS-1 of mast cells. Although an electrophoresis mobility shift assay showed that GATA3 binds to HSS2 *in vitro* [70, 71], two independent genome-wide GATA3 ChIP-seq data analyses failed to detect significant GATA3 binding peak in the CNS-1 region (**Figure 1**) [8, 79].

**Figure 1.** GATA3-dependent epigenetic and transcriptional regulation in the Th2 cytokine gene loci. Epigenetic permissive histone marks (H3K9 acetylation and H3K4 tri-methylation) in the Th2 cytokine loci are shown in Th1 and Th2 cells (GSE28292) using the IGV genome browser (http://www.broadinstitute.org/igv/). GATA3 ChIP-seq data with statistically significant peaks (asterisks) are also shown in Th2 cells. DNA methylation data are shown in CD4+ naïve T, Th1, and Th2 cells (GSE25688). Data from an assay for transposase-accessible chromatin sequencing (ATAC-Seq), which identifies opened chromatin regions, were obtained for lung Th2 cells (GSE77695).

Taken together with the fact that histone acetylation levels are increased with progressive DNA demethylation in the CNS-1 region [61, 80], this region may recruit other critical transcription factors that induce epigenetic modifications and promote IL-4 production in Th2 cells.

**5.3. GATA3-dependent transcriptional regulation of Th2 signature genes**

In addition to regulating chromatin remodeling, GATA3 may induce *Il5* and *Il13* transcription by directly binding to the promoters of these cytokine genes upon TCR re-stimulation [7, 85–87]. In fact, *Gata3* siRNA knockdown just before TCR re-stimulation resulted in reduced expression of *Il5* and *Il13* in established Th2 cells (**Figure 2**). The role of GATA3 in *Il5* and *Il13* transcription was also reported using genetic deletion of the *Gata3* gene. While GATA3 deletion during Th2 differentiation abolished the expression of all Th2 cytokines, GATA3 deletion in established Th2

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**Figure 2.** The effects of GATA3 knockdown on the Th2-specific genes in effector and memory Th2 cells. The effects of GATA3 knockdown on effector Th2 (upper) and memory Th2 (lower) were determined with qRT-PCR (originally published in *PLoS ONE*. Sasaki et al. [9]). The relative expression (GATA3/control siRNA) is rank-ordered and shown as a percentage. The genes indicated in the red bar showed increased GATA3 dependency in memory Th2 cells, while those

in blue showed decreased GATA3 dependency.

HSVa is a TCR re-stimulation-dependent HS site, whose DNase I hypersensitiveness is induced in Th2 cells upon stimulation [72]. HSVa is located 5 kbp downstream of the 3′ end of the *Il4* coding region. Th2 cells generated from the mice in which the genomic region containing both HSVa and HSV (CNS-2) has been deleted display a reduced IL-4 production [81]. Another study reported on the phenotypes of mice with genomes containing the specific deletion of the CNS-2 region [82]. Mice lacking CNS-2 display marked defects in Th2 humoral immune responses. However, the effector Th2 cells involved in tissue responses were not likely to be dependent on CNS-2. In this region, increased histone acetylation levels are observed. In contrast, changes in DNA methylation state are not induced, as DNA is demethylated even in naïve CD4 T cells [80]. By using a conventional ChIP technique, both GATA3 and nuclear factor of activated T cells 1 (NFAT1) have been shown to bind to HSVa in Th2 cells [72]. We and others have performed a GATA3 ChIP-seq analysis and detected GATA3 binding peaks at the HSVa [8, 79], implying that HSVa functions as an important regulatory element through which GATA3 and NFAT1 collaborate to induce IL-4 production in stimulated Th2 cells.

As we reported in 2002, CGRE was originally identified as a region with a 71-bp sequence located 1.6 kbp upstream of the *Il13* gene [73]. The location of CGRE corresponds approximately to the site of HSI. CGRE contains four putative GATA-binding sequences conserved across species [73]. Strong signals of GATA3 binding have been detected by both conventional ChIP assay and ChIP-seq analyses at the CGRE [8, 9, 79]. Interestingly, CGRE is also located at the 5′ edge of the region of histone hyperacetylation, suggesting that GATA3 binds to the CGRE and induces histone acetylation toward the 3′ region of the *Il13* gene. Indeed, GATA3 associates with RNA polymerase II and CBP/p300, which contain histone acetyltransferase activity at this region [73]. In addition, CGRE is located at the 5′ edge of the accessible DNA region detected by ATAC-seq [63]. Thus, the CGRE region may play an important role in *Il13* transcription and in chromatin remodeling at the *Il13* locus. Notably, the Th2 cells generated from CGRE-deficient mice exhibit diminished IL-13 but not IL-4 or IL-5 production [74].

Among several GATA3 binding sites found in the *Il4* gene locus, the strongest GATA3 binding signal was detected at the HSII site located in intron 2 of the *Il4* gene [8]. This region also contains binding sites for STAT5, which has been reported to be important for the maintenance of DNA accessibility of this region in Th2 cells [23, 83]. Correspondingly, a strong ATAC-seq peak was detected at this region in Th2 cells [63]. Recently, a group reported that genetic deletion of HSII resulted in a reduction in IL-4 but not IL-13 production, implying its role in regulating IL-4 production [74]. In addition to histone hyperacetylation induced in this region, H3K4me3 was strongly induced at HSII in Th2 but not Th1 cells [84], suggesting that GATA3 may work together with STAT5 and remodel the chromatin structure at this region. Parallel to changes in histone modifications, progressive DNA demethylation was observed across the *Il4* gene locus. In naïve CD4 T cells, only the promoter region of the *Il4* gene is demethylated, and DNA demethylation extends into the *Il4* gene body during Th2 cell differentiation [80].

#### **5.3. GATA3-dependent transcriptional regulation of Th2 signature genes**

Taken together with the fact that histone acetylation levels are increased with progressive DNA demethylation in the CNS-1 region [61, 80], this region may recruit other critical transcription

HSVa is a TCR re-stimulation-dependent HS site, whose DNase I hypersensitiveness is induced in Th2 cells upon stimulation [72]. HSVa is located 5 kbp downstream of the 3′ end of the *Il4* coding region. Th2 cells generated from the mice in which the genomic region containing both HSVa and HSV (CNS-2) has been deleted display a reduced IL-4 production [81]. Another study reported on the phenotypes of mice with genomes containing the specific deletion of the CNS-2 region [82]. Mice lacking CNS-2 display marked defects in Th2 humoral immune responses. However, the effector Th2 cells involved in tissue responses were not likely to be dependent on CNS-2. In this region, increased histone acetylation levels are observed. In contrast, changes in DNA methylation state are not induced, as DNA is demethylated even in naïve CD4 T cells [80]. By using a conventional ChIP technique, both GATA3 and nuclear factor of activated T cells 1 (NFAT1) have been shown to bind to HSVa in Th2 cells [72]. We and others have performed a GATA3 ChIP-seq analysis and detected GATA3 binding peaks at the HSVa [8, 79], implying that HSVa functions as an important regulatory element through which GATA3 and NFAT1 collaborate to induce IL-4 production

As we reported in 2002, CGRE was originally identified as a region with a 71-bp sequence located 1.6 kbp upstream of the *Il13* gene [73]. The location of CGRE corresponds approximately to the site of HSI. CGRE contains four putative GATA-binding sequences conserved across species [73]. Strong signals of GATA3 binding have been detected by both conventional ChIP assay and ChIP-seq analyses at the CGRE [8, 9, 79]. Interestingly, CGRE is also located at the 5′ edge of the region of histone hyperacetylation, suggesting that GATA3 binds to the CGRE and induces histone acetylation toward the 3′ region of the *Il13* gene. Indeed, GATA3 associates with RNA polymerase II and CBP/p300, which contain histone acetyltransferase activity at this region [73]. In addition, CGRE is located at the 5′ edge of the accessible DNA region detected by ATAC-seq [63]. Thus, the CGRE region may play an important role in *Il13* transcription and in chromatin remodeling at the *Il13* locus. Notably, the Th2 cells generated from CGRE-deficient mice exhibit diminished IL-13 but not IL-4 or IL-5 production [74].

Among several GATA3 binding sites found in the *Il4* gene locus, the strongest GATA3 binding signal was detected at the HSII site located in intron 2 of the *Il4* gene [8]. This region also contains binding sites for STAT5, which has been reported to be important for the maintenance of DNA accessibility of this region in Th2 cells [23, 83]. Correspondingly, a strong ATAC-seq peak was detected at this region in Th2 cells [63]. Recently, a group reported that genetic deletion of HSII resulted in a reduction in IL-4 but not IL-13 production, implying its role in regulating IL-4 production [74]. In addition to histone hyperacetylation induced in this region, H3K4me3 was strongly induced at HSII in Th2 but not Th1 cells [84], suggesting that GATA3 may work together with STAT5 and remodel the chromatin structure at this region. Parallel to changes in histone modifications, progressive DNA demethylation was observed across the *Il4* gene locus. In naïve CD4 T cells, only the promoter region of the *Il4* gene is demethylated, and DNA demethylation extends into the *Il4* gene body during Th2

factors that induce epigenetic modifications and promote IL-4 production in Th2 cells.

198 Gene Expression and Regulation in Mammalian Cells - Transcription From General Aspects

in stimulated Th2 cells.

cell differentiation [80].

In addition to regulating chromatin remodeling, GATA3 may induce *Il5* and *Il13* transcription by directly binding to the promoters of these cytokine genes upon TCR re-stimulation [7, 85–87]. In fact, *Gata3* siRNA knockdown just before TCR re-stimulation resulted in reduced expression of *Il5* and *Il13* in established Th2 cells (**Figure 2**). The role of GATA3 in *Il5* and *Il13* transcription was also reported using genetic deletion of the *Gata3* gene. While GATA3 deletion during Th2 differentiation abolished the expression of all Th2 cytokines, GATA3 deletion in established Th2

**Figure 2.** The effects of GATA3 knockdown on the Th2-specific genes in effector and memory Th2 cells. The effects of GATA3 knockdown on effector Th2 (upper) and memory Th2 (lower) were determined with qRT-PCR (originally published in *PLoS ONE*. Sasaki et al. [9]). The relative expression (GATA3/control siRNA) is rank-ordered and shown as a percentage. The genes indicated in the red bar showed increased GATA3 dependency in memory Th2 cells, while those in blue showed decreased GATA3 dependency.

cells strongly influenced the expression of both IL-5 and IL-13 and induced only a modest reduction in IL-4 production [42]. GATA3 is also crucial for the expression of the Th2 cytokine genes in memory Th2 cells, as *Gata3* siRNA knockdown reduces the transcription of those genes [9]. Furthermore, GATA3 is involved in the transcriptional regulation of other Th2 signature genes in both effector and memory Th2 cells (**Figure 2**). Approximately half of the Th2-specific genes (16 out of 31) showed a significant reduction in their expression in effector Th2 cells (*F2r*, *Mapk12*, *Il1r2*, *Il4*, *Tanc2*, *Ptgir*, *Nfil3*, *Rnf128*, *Asb2*, *Tmtc2*, *Ccnjl*, *Gata3*, *Cyp11a1*, *Il13*, *Ccr8*, and *Il5*) by GATA3 knockdown. In contrast, only the *Tube1* gene showed a significant increase in its expression. These results suggest that a major role of GATA3 is the activation of its target gene transcription.

controlled by both GATA3 and Menin. Interestingly, only *Gzma* was negatively regulated by Menin, while the other nine genes were positively regulated. Although *Gata3* siRNA treatment downregulated the *Gzma* expression, the forced expression of h*GATA3* also reduced the *Gzma* expression for some unknown reason. Seven genes (*Crem*, *Cyp11a1*, *F2r*, *Nfil3*, *Ptgir*, *Rnf128*, and *Tmtc2*) were found to be positively controlled by GATA3 and not affected by Menin deficiency (Group 2). Group 3 consisted of *Spry2* and *S100a*, which were found to be controlled in a Menin-dependent and GATA3-independent manner. For the other 11 genes (*Ccnjl*, *Dusp4*, *Ecm1*, *Epas1*, *Grtp1*, *Il1r2*, *Itgb3*, *Jdp2*, *Penk*, *Plcd1*, and *Tnfrsf8*), neither *Gata3* knockdown nor

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In our ChIP-seq analysis, the direct binding of Menin was observed in most of the 31 Th2 specific genes, except for *Asb2*, *Mapk12*, *Ecm1*, *Grtp1*, and *Plcd1*. Nine of the Menin target genes (*Ccr8*, *Gata3*, *Il4*, *Il5*, *Il13*, *Il24*, *S100a1*, *Tanc2*, and *Tube1*) were positively regulated by Menin, whereas two targets (*Gzma* and *Spry2*) were negatively regulated. No significant effect of Menin deficiency was observed on the other 15 targets (*Ccnjl*, *Crem*, *Cyp11a1*, *Dusp4*, *Epas1*, *F2r*, *Il1r2*, *Itgb3*, *Jdp2*, *Nfil3*, *Ptgir*, *Penk*, *Rnf128*, *Tmtc2*, and *Tnfrsf8*). Several questions remain to be addressed regarding this regulatory network: Are any other factors involved? What recruits Menin to these gene loci? Why does Menin exert a suppressive effect on some target

**Figure 3.** Th2-specific gene regulatory network. The regulatory network formed by Menin- and Th2-specific genes, including GATA3 (originally published in *The Journal of Immunology*. Onodera et al. [10]). Group 1 contains genes that are controlled by both GATA3 and Menin. Genes in Groups 2 and 3 are controlled by either GATA3 or Menin, respectively. Group 4 includes genes that are affected by neither GATA3 knockdown nor Menin knockout. Red arrows indicate the regulatory interactions

that activate the target gene expression, whereas blue lines indicate the suppressive effects for targets.

Menin deficiency had a significant effect on the gene expression (Group 4).

genes? (**Table 1**).

Interestingly, changes in GATA3 dependency are observed during transition from effector to memory cells. In a previous study [9], we compared the GATA3 dependency in Th2-specific genes between effector Th2 cells and *in vivo-*generated memory Th2 cells by *Gata3* siRNA knockdown. GATA3 dependency increased by more than twofold in the *Epas1* and *Il24* genes in memory Th2 cells compared to the effector Th2 cells. In addition, for the *Tube1*, *Rnfl28*, *Ccr8*, and *Il5* genes, the GATA3 dependency decreased by more than twofold. These results indicate that each Th2-specific gene differentially changes its dependency on GATA3 during maturation to memory Th2 cells from effector Th2 cells. The changes in GATA3 dependency, however, do not correlate with dependency itself. For example, *Il5* is a gene with high dependency on GATA3 that shows a decreased dependency in memory Th2 cells. Taken together, these findings indicate that GATA3 is important for maintaining the transcriptional signatures in established Th2 cells.

## **6. A gene regulatory network in fully developed Th2 cells: the interplay between GATA3 and Menin, a component of the Trithorax complex**

As described in Section 4.2, although Menin deficiency had little effect on the ordinary induction of Th2 differentiation, 'Th2 cells' lost their Th2 identity after several cycles of cultivation in the absence of Menin. Our study also revealed that Menin directly bound and epigenetically regulated the *Gata3* gene, suggesting that constant expression of Menin and its binding to the *Gata3* locus is necessary for the maintenance of the Th2 identity. Similar results were obtained with *in vivo*-generated memory Th2 cells, indicating that Menin maintains the memory Th2 cell function during the long-term resting phase. Indeed, Menin-deficient memory Th2 cells show an impaired ability to recruit eosinophils to the lung, causing the attenuation of airway inflammation induced by memory Th2 cells [52].

Since Th2 cells derived from Menin-deficient mice have defects in both Menin and GATA3 expression, whether the lack of Menin, decreased expression of GATA3, or both are responsible for the dysregulation of the Th2-specific gene expression in Menin-deficient cells remains unclear. In a recent study [52], we addressed this point using differentiated Th2 cells with two additional cycles of cultivation (Th2-3rd cells). Consequently, the gene expression profiles under three conditions (i.e. genetic deletion of Menin, *Gata3* siRNA treatment, and retroviral gene transduction of h*GATA3*) were used to classify the Th2-specific genes into four groups (**Figure 3**). *Asb2*, *Ccr8*, *Gzma*, *Il4*, *Il5*, *Il13*, *Il24*, *Mapk12*, *Tanc2*, and *Tube1* were assigned to Group 1, being controlled by both GATA3 and Menin. Interestingly, only *Gzma* was negatively regulated by Menin, while the other nine genes were positively regulated. Although *Gata3* siRNA treatment downregulated the *Gzma* expression, the forced expression of h*GATA3* also reduced the *Gzma* expression for some unknown reason. Seven genes (*Crem*, *Cyp11a1*, *F2r*, *Nfil3*, *Ptgir*, *Rnf128*, and *Tmtc2*) were found to be positively controlled by GATA3 and not affected by Menin deficiency (Group 2). Group 3 consisted of *Spry2* and *S100a*, which were found to be controlled in a Menin-dependent and GATA3-independent manner. For the other 11 genes (*Ccnjl*, *Dusp4*, *Ecm1*, *Epas1*, *Grtp1*, *Il1r2*, *Itgb3*, *Jdp2*, *Penk*, *Plcd1*, and *Tnfrsf8*), neither *Gata3* knockdown nor Menin deficiency had a significant effect on the gene expression (Group 4).

cells strongly influenced the expression of both IL-5 and IL-13 and induced only a modest reduction in IL-4 production [42]. GATA3 is also crucial for the expression of the Th2 cytokine genes in memory Th2 cells, as *Gata3* siRNA knockdown reduces the transcription of those genes [9]. Furthermore, GATA3 is involved in the transcriptional regulation of other Th2 signature genes in both effector and memory Th2 cells (**Figure 2**). Approximately half of the Th2-specific genes (16 out of 31) showed a significant reduction in their expression in effector Th2 cells (*F2r*, *Mapk12*, *Il1r2*, *Il4*, *Tanc2*, *Ptgir*, *Nfil3*, *Rnf128*, *Asb2*, *Tmtc2*, *Ccnjl*, *Gata3*, *Cyp11a1*, *Il13*, *Ccr8*, and *Il5*) by GATA3 knockdown. In contrast, only the *Tube1* gene showed a significant increase in its expression. These

200 Gene Expression and Regulation in Mammalian Cells - Transcription From General Aspects

results suggest that a major role of GATA3 is the activation of its target gene transcription.

**6. A gene regulatory network in fully developed Th2 cells: the**

of airway inflammation induced by memory Th2 cells [52].

**complex**

**interplay between GATA3 and Menin, a component of the Trithorax**

As described in Section 4.2, although Menin deficiency had little effect on the ordinary induction of Th2 differentiation, 'Th2 cells' lost their Th2 identity after several cycles of cultivation in the absence of Menin. Our study also revealed that Menin directly bound and epigenetically regulated the *Gata3* gene, suggesting that constant expression of Menin and its binding to the *Gata3* locus is necessary for the maintenance of the Th2 identity. Similar results were obtained with *in vivo*-generated memory Th2 cells, indicating that Menin maintains the memory Th2 cell function during the long-term resting phase. Indeed, Menin-deficient memory Th2 cells show an impaired ability to recruit eosinophils to the lung, causing the attenuation

Since Th2 cells derived from Menin-deficient mice have defects in both Menin and GATA3 expression, whether the lack of Menin, decreased expression of GATA3, or both are responsible for the dysregulation of the Th2-specific gene expression in Menin-deficient cells remains unclear. In a recent study [52], we addressed this point using differentiated Th2 cells with two additional cycles of cultivation (Th2-3rd cells). Consequently, the gene expression profiles under three conditions (i.e. genetic deletion of Menin, *Gata3* siRNA treatment, and retroviral gene transduction of h*GATA3*) were used to classify the Th2-specific genes into four groups (**Figure 3**). *Asb2*, *Ccr8*, *Gzma*, *Il4*, *Il5*, *Il13*, *Il24*, *Mapk12*, *Tanc2*, and *Tube1* were assigned to Group 1, being

Interestingly, changes in GATA3 dependency are observed during transition from effector to memory cells. In a previous study [9], we compared the GATA3 dependency in Th2-specific genes between effector Th2 cells and *in vivo-*generated memory Th2 cells by *Gata3* siRNA knockdown. GATA3 dependency increased by more than twofold in the *Epas1* and *Il24* genes in memory Th2 cells compared to the effector Th2 cells. In addition, for the *Tube1*, *Rnfl28*, *Ccr8*, and *Il5* genes, the GATA3 dependency decreased by more than twofold. These results indicate that each Th2-specific gene differentially changes its dependency on GATA3 during maturation to memory Th2 cells from effector Th2 cells. The changes in GATA3 dependency, however, do not correlate with dependency itself. For example, *Il5* is a gene with high dependency on GATA3 that shows a decreased dependency in memory Th2 cells. Taken together, these findings indicate that GATA3 is important for maintaining the transcriptional signatures in established Th2 cells.

In our ChIP-seq analysis, the direct binding of Menin was observed in most of the 31 Th2 specific genes, except for *Asb2*, *Mapk12*, *Ecm1*, *Grtp1*, and *Plcd1*. Nine of the Menin target genes (*Ccr8*, *Gata3*, *Il4*, *Il5*, *Il13*, *Il24*, *S100a1*, *Tanc2*, and *Tube1*) were positively regulated by Menin, whereas two targets (*Gzma* and *Spry2*) were negatively regulated. No significant effect of Menin deficiency was observed on the other 15 targets (*Ccnjl*, *Crem*, *Cyp11a1*, *Dusp4*, *Epas1*, *F2r*, *Il1r2*, *Itgb3*, *Jdp2*, *Nfil3*, *Ptgir*, *Penk*, *Rnf128*, *Tmtc2*, and *Tnfrsf8*). Several questions remain to be addressed regarding this regulatory network: Are any other factors involved? What recruits Menin to these gene loci? Why does Menin exert a suppressive effect on some target genes? (**Table 1**).

**Figure 3.** Th2-specific gene regulatory network. The regulatory network formed by Menin- and Th2-specific genes, including GATA3 (originally published in *The Journal of Immunology*. Onodera et al. [10]). Group 1 contains genes that are controlled by both GATA3 and Menin. Genes in Groups 2 and 3 are controlled by either GATA3 or Menin, respectively. Group 4 includes genes that are affected by neither GATA3 knockdown nor Menin knockout. Red arrows indicate the regulatory interactions that activate the target gene expression, whereas blue lines indicate the suppressive effects for targets.

**7. Conclusions**

**Abbreviations**

[47].

Since the human genome project was completed in 2003, the human genomic DNA database has become accessible to researchers [109]. Open access to the reference genomes of humans, mice, and other organisms encourages scientists to develop elegant technologies, including ChIP-seq and high-throughput sequencing of RNA (RNA-seq) [110]. This technique enables us to analyze the epigenetic status of each population of cells on a genome-wide scale. Many scientists have tried to use this technique to clarify the functional roles of epigenetic modifications in gene expression, particularly in the fields of developmental biology and immunology

The Interplay between Transcription Factors and Epigenetic Modifications in Th2 Cells

http://dx.doi.org/10.5772/intechopen.73027

203

Recently, we identified several important principles between the binding positions of PcG and TrxG proteins and the gene expression [52]; a binding pattern in which PcG binds upstream and TrxG binds downstream of the transcription start site is frequently found at highly expressed genes, and a binding pattern in which PcG and TrxG bind to opposite positions is frequently found at low-expressed genes in T lymphocytes. We hope that these findings will prove useful for understanding how CD4+ T cells acquire effector functions and identifying new therapeutic targets for treating allergic diseases, such as asthma, allergic rhinitis, food allergy, and atopic dermatitis. A recently developed epigenetic editing technique using the CRISPR/Cas9 system now allows us to modify epigenetic marks in a site-specific manner [111]. In the future,

we may use this technique to treat various diseases cause by epigenetic alternations.

ChIP-Seq chromatin immunoprecipitation followed by massively parallel sequencing

ATAC-Seq assay for transposase-accessible chromatin sequencing

CNS conserved non-coding sequence

HS DNase I hypersensitive site

PRC Polycomb repressive complex

STAT signal transducer and activator of transcription

IL interleukin

Th helper T cell

TrxG Trithorax group

PcG Polycomb group

H3K27me3 trimethylated histone H3 lysine 27 H3K4me3 trimethylated histone H3 lysine 4

**Table 1.** Summary of the target genes of the GATA3 and Menin with functions of the encoded proteins (based on https:// www.ncbi.nlm.nih.gov/gene).

## **7. Conclusions**

**RefSeq ID Gene symbol Group GO term (function, process, or component)**

202 Gene Expression and Regulation in Mammalian Cells - Transcription From General Aspects

NM\_010370 Gzma 1 Serine-type peptidase activity [90]

NM\_007720 Ccr8 1 C-C chemokine receptor activity [92]

NM\_181071 Tanc2 1 In utero embryonic development [94]

NM\_008967 Ptgir 2 G-protein coupled receptor activity

NM\_023270 Rnf128 2 Ubiquitin protein ligase activity [99]

NM\_007899 Ecm1 4 Interleukin-2 receptor binding [102]

NM\_010555 Il1r2 4 Interleukin-1 receptor activity [104]

NM\_177368 Tmtc2 2 Calcium ion homeostasis

NM\_011309 S100a1 3 Protein binding [100]

NM\_001045530 Ccnjl 4 Nucleus component

NM\_025768 Grtp1 4 Rab GTPase binding

www.ncbi.nlm.nih.gov/gene).

NM\_001002927 Penk 4 Aggressive behavior [107]

NM\_010169 F2r 2 G-protein alpha-/beta-subunit binding [97]

NM\_017373 Nflil3 2 RNA polymerase II core promoter sequence-specific DNA binding [95]

NM\_019779 Cyp11a1 2 Cholesterol monooxygenase (side-chain-cleaving) activity [98]

NM\_013498 Crem 2 Core promoter sequence-specific DNA binding [96]

NM\_011897 Spry2 3 Negative regulation of ERK1 and ERK2 cascade [101]

NM\_176933 Dusp4 4 MAP kinase tyrosine/serine/threonine phosphatase activity

NM\_030887 Jdp2 4 RNA polymerase II proximal promoter sequence-specific DNA binding [108]

**Table 1.** Summary of the target genes of the GATA3 and Menin with functions of the encoded proteins (based on https://

NM\_009401 Tnfsf8 4 Tumor necrosis factor-activated receptor activity

NM\_016780 Itgb3 4 Alpha9-beta1 integrin-ADAM8 complex [103]

NM\_010137 Epas1 4 DNA binding transcription factor activity [105]

NM\_019676 Plcd1 4 Phosphatidylinositol phosphate binding [106]

NM\_023049 Asb2 1 Contributes to ubiquitin protein ligase activity [89]

NM\_008355 Il13 1 Cytokine activity NM\_010558 Il5 1 Cytokine activity [88]

NM\_028006 Tube1 1 GTPase activity NM\_013871 Mapk12 1 MAP kinase activity

NM\_053095 Il24 1 Cytokine activity [91]

NM\_021283 Il4 1 Cytokine activity [93]

Since the human genome project was completed in 2003, the human genomic DNA database has become accessible to researchers [109]. Open access to the reference genomes of humans, mice, and other organisms encourages scientists to develop elegant technologies, including ChIP-seq and high-throughput sequencing of RNA (RNA-seq) [110]. This technique enables us to analyze the epigenetic status of each population of cells on a genome-wide scale. Many scientists have tried to use this technique to clarify the functional roles of epigenetic modifications in gene expression, particularly in the fields of developmental biology and immunology [47].

Recently, we identified several important principles between the binding positions of PcG and TrxG proteins and the gene expression [52]; a binding pattern in which PcG binds upstream and TrxG binds downstream of the transcription start site is frequently found at highly expressed genes, and a binding pattern in which PcG and TrxG bind to opposite positions is frequently found at low-expressed genes in T lymphocytes. We hope that these findings will prove useful for understanding how CD4+ T cells acquire effector functions and identifying new therapeutic targets for treating allergic diseases, such as asthma, allergic rhinitis, food allergy, and atopic dermatitis. A recently developed epigenetic editing technique using the CRISPR/Cas9 system now allows us to modify epigenetic marks in a site-specific manner [111]. In the future, we may use this technique to treat various diseases cause by epigenetic alternations.

## **Abbreviations**

## **Author details**

Atsushi Onodera1,2, Kota Kokubo<sup>1</sup> and Toshinori Nakayama<sup>1</sup> \*

\*Address all correspondence to<EMAIL_ADDRESS>
1 Department of Immunology, Graduate School of Medicine, Chiba University, Chuo-ku, Chiba, Japan

[12] Goenka S, Kaplan MH. Transcriptional regulation by STAT6. Immunologic Research.

The Interplay between Transcription Factors and Epigenetic Modifications in Th2 Cells

http://dx.doi.org/10.5772/intechopen.73027

205

[13] Hebenstreit D, Wirnsberger G, Horejs-Hoeck J, Duschl A. Signaling mechanisms, interaction partners, and target genes of STAT6. Cytokine & Growth Factor Reviews. 2006;**17**(3):

[14] Maier E, Duschl A, Horejs-Hoeck J. STAT6-dependent and -independent mechanisms in

[15] Ehret GB, Reichenbach P, Schindler U, Horvath CM, Fritz S, Nabholz M, et al. DNA binding specificity of different STAT proteins. Comparison of in vitro specificity with

[16] Nguyen VT, Benveniste EN. IL-4-activated STAT-6 inhibits IFN-gamma-induced CD40 gene expression in macrophages/microglia. Journal of Immunology. 2000;**165**(11):

[17] Bennett BL, Cruz R, Lacson RG, Manning AM. Interleukin-4 suppression of tumor necrosis factor alpha-stimulated E-selectin gene transcription is mediated by STAT6 antagonism of NF-kappaB. The Journal of Biological Chemistry. 1997;**272**(15):10212-10219

[18] Elo LL, Jarvenpaa H, Tuomela S, Raghav S, Ahlfors H, Laurila K, et al. Genome-wide profiling of interleukin-4 and STAT6 transcription factor regulation of human Th2 cell

[19] O'Shea JJ, Lahesmaa R, Vahedi G, Laurence A, Kanno Y. Genomic views of STAT function in CD4+ T helper cell differentiation. Nature Reviews. Immunology. 2011;**11**(4):239-250

[20] Kopf M, Le Gros G, Bachmann M, Lamers MC, Bluethmann H, Kohler G. Disruption of the murine IL-4 gene blocks Th2 cytokine responses. Nature. 1993;**362**(6417):245-248

[21] Wurster AL, Tanaka T, Grusby MJ. The biology of Stat4 and Stat6. Oncogene. 2000;**19**(21):

[22] Takeda K, Tanaka T, Shi W, Matsumoto M, Minami M, Kashiwamura S, et al. Essential

[23] Cote-Sierra J, Foucras G, Guo L, Chiodetti L, Young HA, Hu-Li J, et al. Interleukin 2 plays a central role in Th2 differentiation. Proceedings of the National Academy of Sciences of

[24] Stritesky GL, Muthukrishnan R, Sehra S, Goswami R, Pham D, Travers J, et al. The transcription factor STAT3 is required for T helper 2 cell development. Immunity. 2011;**34**(1):

[25] Mosmann TR, Coffman RL.TH1 and TH2 cells: Different patterns of lymphokine secretion lead to different functional properties. Annual Review of Immunology. 1989;**7**:145-173

[26] Reiner SL, Locksley RM. The regulation of immunity to Leishmania major. Annual

role of Stat6 in IL-4 signalling. Nature. 1996;**380**(6575):627-630

the United States of America. 2004;**101**(11):3880-3885

Review of Immunology. 1995;**13**:151-177

programming. Immunity. 2010;**32**(6):852-862

natural target sites. The Journal of Biological Chemistry. 2001;**276**(9):6675-6688

Th2 polarization. European Journal of Immunology. 2012;**42**(11):2827-2833

2011;**50**(1):87-96

173-188

6235-6243

2577-2584

39-49

2 Institue for Global Prominent Research, Chiba University, Inage-ku, Chiba, Japan

#### **References**

[12] Goenka S, Kaplan MH. Transcriptional regulation by STAT6. Immunologic Research. 2011;**50**(1):87-96

**Author details**

Chiba, Japan

**References**

477-485

Atsushi Onodera1,2, Kota Kokubo<sup>1</sup>

\*Address all correspondence to<EMAIL_ADDRESS>
204 Gene Expression and Regulation in Mammalian Cells - Transcription From General Aspects

Review of Immunology. 2010;**28**:445-489

and Toshinori Nakayama<sup>1</sup>

[1] Zhu J, Yamane H, Paul WE. Differentiation of effector CD4 T cell populations (\*). Annual

[2] Gu C, Wu L, Li X. IL-17 family: Cytokines, receptors and signaling. Cytokine. 2013;**64**(2):

[3] Nakayama T, Hirahara K, Onodera A, Endo Y, Hosokawa H, Shinoda K, et al. Th2 cells

[4] Szabo SJ, Kim ST, Costa GL, Zhang X, Fathman CG, Glimcher LH. A novel transcription

[5] Kaplan MH, Schindler U, Smiley ST, Grusby MJ. Stat6 is required for mediating responses

[6] Zheng W, Flavell RA. The transcription factor GATA-3 is necessary and sufficient for

[7] Zhang DH, Cohn L, Ray P, Bottomly K, Ray A. Transcription factor GATA-3 is differentially expressed in murine Th1 and Th2 cells and controls Th2-specific expression of the interleukin-5 gene. The Journal of Biological Chemistry. 1997;**272**(34):21597-21603 [8] Horiuchi S, Onodera A, Hosokawa H, Watanabe Y, Tanaka T, Sugano S, et al. Genomewide analysis reveals unique regulation of transcription of Th2-specific genes by GATA3.

[9] Sasaki T, Onodera A, Hosokawa H, Watanabe Y, Horiuchi S, Yamashita J, et al. Genomewide gene expression profiling revealed a critical role for GATA3 in the maintenance of the Th2 cell identity. PLoS One. 2013;**8**(6):e66468. DOI: 10.1371/journal.pone.0066468

[10] Onodera A, Kiuchi M, Kokubo K, Kato M, Ogino T, Horiuchi S, et al. Menin controls the memory Th2 cell function by maintaining the epigenetic integrity of Th2 cells. Journal of Immunology. 2017;**199**(3):1153-1162. Copyright © [2017] The American Association of

[11] Pai SY, Truitt ML, Ho IC. GATA-3 deficiency abrogates the development and maintenance of T helper type 2 cells. Proceedings of the National Academy of Sciences of the

in health and disease. Annual Review of Immunology. 2017;**35**:53-84

factor, T-bet, directs Th1 lineage commitment. Cell. 2000;**100**(6):655-669

to IL-4 and for development of Th2 cells. Immunity. 1996;**4**(3):313-319

Th2 cytokine gene expression in CD4 T cells. Cell. 1997;**89**(4):587-596

Journal of Immunology. 2011;**186**(11):6378-6389

United States of America. 2004;**101**(7):1993-1998

Immunologists, Inc

1 Department of Immunology, Graduate School of Medicine, Chiba University, Chuo-ku,

2 Institue for Global Prominent Research, Chiba University, Inage-ku, Chiba, Japan

\*

[27] Ho IC, Tai TS, Pai SY. GATA3 and the T-cell lineage: Essential functions before and after T-helper-2-cell differentiation. Nature Reviews. Immunology. 2009;**9**(2):125-135

[41] Inami M, Yamashita M, Tenda Y, Hasegawa A, Kimura M, Hashimoto K, et al. CD28 costimulation controls histone hyperacetylation of the interleukin 5 gene locus in devel-

The Interplay between Transcription Factors and Epigenetic Modifications in Th2 Cells

http://dx.doi.org/10.5772/intechopen.73027

207

[42] Zhu J, Min B, Hu-Li J, Watson CJ, Grinberg A, Wang Q, et al. Conditional deletion of Gata3 shows its essential function in T(H)1-T(H)2 responses. Nature Immunology. 2004;**5**(11):

[43] Nakayama T, Yamashita M. Critical role of the Polycomb and Trithorax complexes in the maintenance of CD4 T cell memory. Seminars in Immunology. 2009;**21**(2):78-83 [44] Onodera A, Nakayama T. Epigenetics of T cells regulated by Polycomb/Trithorax mol-

[45] Di Croce L, Helin K. Transcriptional regulation by Polycomb group proteins. Nature

[46] Mohan M, Herz HM, Shilatifard A. SnapShot: Histone lysine methylase complexes. Cell.

[47] Steffen PA, Ringrose L. What are memories made of? How Polycomb and Trithorax proteins mediate epigenetic memory. Nature Reviews. Molecular Cell Biology.

[48] Hopkin AS, Gordon W, Klein RH, Espitia F, Daily K, Zeller M, et al. GRHL3/GET1 and trithorax group members collaborate to activate the epidermal progenitor differentiation

[49] Wang H, Wang L, Erdjument-Bromage H, Vidal M, Tempst P, Jones RS, et al. Role of histone H2A ubiquitination in Polycomb silencing. Nature. 2004;**431**(7010):873-878 [50] Tumes DJ, Onodera A, Suzuki A, Shinoda K, Endo Y, Iwamura C, et al. The polycomb protein Ezh2 regulates differentiation and plasticity of CD4(+) T helper type 1 and type

[51] Onodera A, Yamashita M, Endo Y, Kuwahara M, Tofukuji S, Hosokawa H, et al. STAT6 mediated displacement of polycomb by trithorax complex establishes long-term maintenance of GATA3 expression in T helper type 2 cells. The Journal of Experimental

[52] Onodera A, Tumes DJ, Watanabe Y, Hirahara K, Kaneda A, Sugiyama F, et al. Spatial interplay between polycomb and trithorax complexes controls transcriptional activity in

[53] Schuettengruber B, Martinez AM, Iovino N, Cavalli G. Trithorax group proteins: Switching genes on and keeping them active. Nature Reviews. Molecular Cell Biology.

[54] Matkar S, Thiel A, Hua X. Menin: A scaffold protein that controls gene expression and

[55] Balogh K, Racz K, Patocs A, Hunyady L. Menin and its interacting proteins: Elucidation of menin function. Trends in Endocrinology and Metabolism. 2006;**17**(9):357-364

T lymphocytes. Molecular and Cellular Biology. 2015;**35**(22):3841-3853

cell signaling. Trends in Biochemical Sciences. 2013;**38**(8):394-402

ecules. Trends in Molecular Medicine. 2015;**21**(5):330-340

Structural & Molecular Biology. 2013;**20**(10):1147-1155

program. PLoS Genetics. 2012;**8**(7):e1002829

2 cells. Immunity. 2013;**39**(5):819-832

Medicine. 2010;**207**(11):2493-2506

2011;**12**(12):799-814

oping th2 cells. The Journal of Biological Chemistry. 2004;**279**(22):23123-23133

1157-1165

2012;**149**(2):498-4e1

2014;**15**(5):340-356

[41] Inami M, Yamashita M, Tenda Y, Hasegawa A, Kimura M, Hashimoto K, et al. CD28 costimulation controls histone hyperacetylation of the interleukin 5 gene locus in developing th2 cells. The Journal of Biological Chemistry. 2004;**279**(22):23123-23133

[27] Ho IC, Tai TS, Pai SY. GATA3 and the T-cell lineage: Essential functions before and after T-helper-2-cell differentiation. Nature Reviews. Immunology. 2009;**9**(2):125-135 [28] Korn T, Bettelli E, Oukka M, Kuchroo VK. IL-17 and Th17 cells. Annual Review of Immu-

[29] Szabo SJ, Sullivan BM, Stemmann C, Satoskar AR, Sleckman BP, Glimcher LH. Distinct effects of T-bet in TH1 lineage commitment and IFN-gamma production in CD4 and

[30] Lee HJ, Takemoto N, Kurata H, Kamogawa Y, Miyatake S, O'Garra A, et al. GATA-3 induces T helper cell type 2 (Th2) cytokine expression and chromatin remodeling in

[32] Hernandez-Hoyos G, Anderson MK, Wang C, Rothenberg EV, Alberola-Ila J. GATA-3 expression is controlled by TCR signals and regulates CD4/CD8 differentiation. Immunity.

[33] Yamamoto M, Ko LJ, Leonard MW, Beug H, Orkin SH, Engel JD. Activity and tissue-specific expression of the transcription factor NF-E1 multigene family. Genes &

[34] Hosoya T, Maillard I, Engel JD.From the cradle to the grave: Activities of GATA-3 throughout T-cell development and differentiation. Immunological Reviews. 2010;**238**(1):110-125

[35] Ouyang W, Ranganath SH, Weindel K, Bhattacharya D, Murphy TL, Sha WC, et al. Inhibition of Th1 development mediated by GATA-3 through an IL-4-independent

[36] Ouyang W, Lohning M, Gao Z, Assenmacher M, Ranganath S, Radbruch A, et al. Stat6 independent GATA-3 autoactivation directs IL-4-independent Th2 development and

[37] Hosokawa H, Kimura MY, Shinnakasu R, Suzuki A, Miki T, Koseki H, et al. Regulation of Th2 cell development by Polycomb group gene bmi-1 through the stabilization of

[38] Shinnakasu R, Yamashita M, Shinoda K, Endo Y, Hosokawa H, Hasegawa A, et al. Critical YxKxHxxxRP motif in the C-terminal region of GATA3 for its DNA binding and

[39] Yamashita M, Shinnakasu R, Asou H, Kimura M, Hasegawa A, Hashimoto K, et al. Ras-ERK MAPK cascade regulates GATA3 stability and Th2 differentiation through ubiquitin-proteasome pathway. The Journal of Biological Chemistry. 2005;**280**(33):29409-29419

[40] Yamashita M, Ukai-Tadenuma M, Miyamoto T, Sugaya K, Hosokawa H, Hasegawa A, et al. Essential role of GATA3 for the maintenance of type 2 helper T (Th2) cytokine production and chromatin remodeling at the Th2 cytokine gene loci. The Journal of

committed Th1 cells. The Journal of Experimental Medicine. 2000;**192**(1):105-115 [31] Pai SY, Truitt ML, Ting CN, Leiden JM, Glimcher LH, Ho IC. Critical roles for transcription factor GATA-3 in thymocyte development.  Immunity. 1998;**9**(5):745-755

commitment. Immunity. 2000;**12**(1):27-37

GATA3. Journal of Immunology. 2006;**177**(11):7656-7664

function. Journal of Immunology. 2006;**177**(9):5801-5810

Biological Chemistry. 2004;**279**(26):26983-26990

CD8 T cells. Science. 2002;**295**(5553):338-342

206 Gene Expression and Regulation in Mammalian Cells - Transcription From General Aspects

[56] Nakata Y, Brignier AC, Jin S, Shen Y, Rudnick SI, Sugita M, et al. C-Myb, Menin, GATA-3, and MLL form a dynamic transcription complex that plays a pivotal role in human T helper type 2 cell development. Blood. 2010;**116**(8):1280-1290

[71] Takemoto N, Arai K, Miyatake S. Cutting edge: The differential involvement of the N-finger of GATA-3 in chromatin remodeling and transactivation during Th2 develop-

The Interplay between Transcription Factors and Epigenetic Modifications in Th2 Cells

http://dx.doi.org/10.5772/intechopen.73027

209

[72] Agarwal S, Avni O, Rao A. Cell-type-restricted binding of the transcription factor NFAT

[73] Yamashita M, Ukai-Tadenuma M, Kimura M, Omori M, Inami M, Taniguchi M, et al. Identification of a conserved GATA3 response element upstream proximal from the interleukin-13 gene locus. The Journal of Biological Chemistry. 2002;**277**(44):42399-42408

[74] Tanaka S, Motomura Y, Suzuki Y, Yagi R, Inoue H, Miyatake S, et al. The enhancer HS2 critically regulates GATA-3-mediated Il4 transcription in T(H)2 cells. Nature Immu-

[75] Takemoto N, Koyano-Nakagawa N, Yokota T, Arai N, Miyatake S, Arai K. Th2-specific DNase I-hypersensitive sites in the murine IL-13 and IL-4 intergenic region. International

[76] Lee GR, Kim ST, Spilianakis CG, Fields PE, Flavell RA. T helper cell differentiation:

[77] Mohrs M, Blankespoor CM, Wang ZE, Loots GG, Afzal V, Hadeiba H, et al. Deletion of a coordinate regulator of type 2 cytokine expression in mice. Nature Immunology.

[78] Monticelli S, Lee DU, Nardone J, Bolton DL, Rao A. Chromatin-based regulation of cytokine transcription in Th2 cells and mast cells. International Immunology. 2005;**17**(11):

[79] Wei G, Abraham BJ, Yagi R, Jothi R, Cui K, Sharma S, et al. Genome-wide analyses of transcription factor GATA3-mediated gene regulation in distinct T cell types. Immunity.

[80] Lee DU, Agarwal S, Rao A. Th2 lineage commitment and efficient IL-4 production involves extended demethylation of the IL-4 gene. Immunity. 2002;**16**(5):649-660 [81] Solymar DC, Agarwal S, Bassing CH, Alt FW, Rao A. A 3' enhancer in the IL-4 gene regulates cytokine production by Th2 cells and mast cells. Immunity. 2002;**17**(1):41-50 [82] Vijayanand P, Seumois G, Simpson LJ, Abdul-Wajid S, Baumjohann D, Panduro M, et al. Interleukin-4 production by follicular helper T cells requires the conserved Il4 enhancer

[83] Zhu J, Cote-Sierra J, Guo L, Paul WE. Stat5 activation plays a critical role in Th2 differen-

[84] Wei G, Wei L, Zhu J, Zang C, Hu-Li J, Yao Z, et al. Global mapping of H3K4me3 and H3K27me3 reveals specificity and plasticity in lineage fate determination of differentiat-

[85] Lee HJ, O'Garra A, Arai K, Arai N. Characterization of cis-regulatory elements and nuclear factors conferring Th2-specific expression of the IL-5 gene: A role for a GATA-

hypersensitivity site V. Immunity. 2012;**36**(2):175-187

ing CD4+ T cells. Immunity. 2009;**30**(1):155-167

binding protein. Journal of Immunology. 1998;**160**(5):2343-2352

tiation. Immunity. 2003;**19**(5):739-748

Regulation by cis elements and epigenetics. Immunity. 2006;**24**(4):369-379

ment. Journal of Immunology. 2002;**169**(8):4103-4107

nology. 2011;**12**(1):77-85

2001;**2**(9):842-847

2011;**35**(2):299-311

1513-1524

Immunology. 1998;**10**(12):1981-1985

to a distal IL-4 enhancer in vivo. Immunity. 2000;**12**(6):643-652

[71] Takemoto N, Arai K, Miyatake S. Cutting edge: The differential involvement of the N-finger of GATA-3 in chromatin remodeling and transactivation during Th2 development. Journal of Immunology. 2002;**169**(8):4103-4107

[56] Nakata Y, Brignier AC, Jin S, Shen Y, Rudnick SI, Sugita M, et al. C-Myb, Menin, GATA-3, and MLL form a dynamic transcription complex that plays a pivotal role in human T

[57] Zhang JA, Mortazavi A, Williams BA, Wold BJ, Rothenberg EV. Dynamic transformations of genome-wide epigenetic marking and transcriptional control establish T cell

[58] Margueron R, Reinberg D. The polycomb complex PRC2 and its mark in life. Nature.

[59] Ansel KM, Djuretic I, Tanasa B, Rao A. Regulation of Th2 differentiation and Il4 locus

[60] Scheinman EJ, Avni O. Transcriptional regulation of GATA3 in T helper cells by the integrated activities of transcription factors downstream of the interleukin-4 receptor and T

[61] Deaton AM, Webb S, Kerr AR, Illingworth RS, Guy J, Andrews R, et al. Cell type-specific DNA methylation at intragenic CpG islands in the immune system. Genome Research.

[62] Wei L, Vahedi G, Sun HW, Watford WT, Takatori H, Ramos HL, et al. Discrete roles of STAT4 and STAT6 transcription factors in tuning epigenetic modifications and transcrip-

[63] Shih HY, Sciume G, Mikami Y, Guo L, Sun HW, Brooks SR, et al. Developmental acquisition of regulomes underlies innate lymphoid cell functionality. Cell. 2016;**165**(5):1120-1133

[64] Yamashita M, Hirahara K, Shinnakasu R, Hosokawa H, Norikane S, Kimura MY, et al. Crucial role of MLL for the maintenance of memory T helper type 2 cell responses.

[65] Liu J, Cao L, Chen J, Song S, Lee IH, Quijano C, et al. Bmi1 regulates mitochondrial function and the DNA damage response pathway. Nature. 2009;**459**(7245):387-392

[66] Koyanagi M, Baguet A, Martens J, Margueron R, Jenuwein T, Bix M. EZH2 and histone 3 trimethyl lysine 27 associated with Il4 and Il13 gene silencing in Th1 cells. The Journal

[67] Allan RS, Zueva E, Cammas F, Schreiber HA, Masson V, Belz GT, et al. An epigenetic silencing pathway controlling T helper 2 cell lineage commitment. Nature. 2012;**487**(7406):

[68] Yagi R, Zhu J, Paul WE. An updated view on transcription factor GATA3-mediated regulation of Th1 and Th2 cell differentiation. International Immunology. 2011;**23**(7):415-420

[69] Yu M, Riva L, Xie H, Schindler Y, Moran TB, Cheng Y, et al. Insights into GATA-1 mediated gene activation versus repression via genome-wide chromatin occupancy

[70] Takemoto N, Kamogawa Y, Jun Lee H, Kurata H, Arai KI, O'Garra A, et al. Cutting edge: Chromatin remodeling at the IL-4/IL-13 intergenic regulatory region for Th2-specific

cytokine gene cluster. Journal of Immunology. 2000;**165**(12):6687-6691

cell receptor. The Journal of Biological Chemistry. 2009;**284**(5):3037-3048

tion during T helper cell differentiation. Immunity. 2010;**32**(6):840-851

helper type 2 cell development. Blood. 2010;**116**(8):1280-1290

208 Gene Expression and Regulation in Mammalian Cells - Transcription From General Aspects

accessibility. Annual Review of Immunology. 2006;**24**:607-656

identity. Cell. 2012;**149**(2):467-482

2011;**469**(7330):343-349

2011;**21**(7):1074-1086

Immunity. 2006;**24**(5):611-622

249-253

of Biological Chemistry. 2005;**280**(36):31470-31477

analysis. Molecular Cell. 2009;**36**(4):682-695

[86] Schwenger GT, Fournier R, Kok CC, Mordvinov VA, Yeoman D, Sanderson CJ. GATA-3 has dual regulatory functions in human interleukin-5 transcription. The Journal of Biological Chemistry. 2001;**276**(51):48502-48509

[99] Borchers AG, Hufton AL, Eldridge AG, Jackson PK, Harland RM, Baker JC. The E3 ubiquitin ligase GREUL1 anteriorizes ectoderm during Xenopus development.

The Interplay between Transcription Factors and Epigenetic Modifications in Th2 Cells

http://dx.doi.org/10.5772/intechopen.73027

211

[100] Tarabykina S, Kriajevska M, Scott DJ, Hill TJ, Lafitte D, Derrick PJ, et al. Heterocomplex formation between metastasis-related protein S100A4 (Mts1) and S100A1 as revealed

[101] Gross I, Bassit B, Benezra M, Licht JD. Mammalian sprouty proteins inhibit cell growth and differentiation by preventing ras activation. The Journal of Biological Chemistry.

[102] Li Z, Zhang Y, Liu Z, Wu X, Zheng Y, Tao Z, et al. ECM1 controls T(H)2 cell egress from lymph nodes through re-expression of S1P(1). Nature Immunology. 2011;**12**(2):178-185

[103] Rao H, Lu G, Kajiya H, Garcia-Palacios V, Kurihara N, Anderson J, et al. Alpha9beta1: A novel osteoclast integrin that regulates osteoclast formation and function. Journal of

[104] Zheng Y, Humphry M, Maguire JJ, Bennett MR, Clarke MC. Intracellular interleukin-1 receptor 2 binding prevents cleavage and activity of interleukin-1alpha, controlling

[105] Elvert G, Kappel A, Heidenreich R, Englmeier U, Lanz S, Acker T, et al. Cooperative interaction of hypoxia-inducible factor-2alpha (HIF-2alpha ) and Ets-1 in the transcriptional activation of vascular endothelial growth factor receptor-2 (Flk-1). The Journal of

[106] Kim NY, Ahn SJ, Kim MS, Seo JS, Kim BS, Bak HJ, et al. PLC-delta1-lf, a novel N-terminal

[107] Konig M, Zimmer AM, Steiner H, Holmes PV, Crawley JN, Brownstein MJ, et al. Pain responses, anxiety and aggression in mice deficient in pre-proenkephalin. Nature.

[108] Jin C, Ugai H, Song J, Murata T, Nili F, Sun K, et al. Identification of mouse Jun dimerization protein 2 as a novel repressor of ATF-2. FEBS Letters. 2001;**489**(1):34-41

[109] Collins FS, Green ED, Guttmacher AE, Guyer MS. A vision for the future of genomics

[110] Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, et al. High-resolution profiling of histone methylations in the human genome. Cell. 2007;**129**(4):823-837

[111] Thakore PI, D'Ippolito AM, Song L, Safi A, Shivakumar NK, Kabadi AM, et al. Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory

necrosis-induced sterile inflammation. Immunity. 2013;**38**(2):285-295

extended phospholipase C-delta1. Gene. 2013;**528**(2):170-177

by the yeast two-hybrid system. FEBS Letters. 2000;**475**(3):187-191

Developmental Biology. 2002;**251**(2):395-408

Bone and Mineral Research. 2006;**21**(10):1657-1665

Biological Chemistry. 2003;**278**(9):7520-7530

research. Nature. 2003;**422**(6934):835-847

elements. Nature Methods. 2015;**12**(12):1143-1149

2001;**276**(49):46460-46468

1996;**383**(6600):535-538