Regulator of histone methyltransferase complexes that plays an essential role in embryonic development, including heart and liver development, neural tube fusion process and hematopoiesis (PubMed:10807864, PubMed:12852854, PubMed:12890668, PubMed:15542826, PubMed:15870077, PubMed:19010785, PubMed:20064375, PubMed:20064376, PubMed:20075857). Acts as an accessory subunit for the core PRC2 (Polycomb repressive complex 2) complex, which mediates histone H3K27 (H3K27me3) trimethylation on chromatin (PubMed:20064376, PubMed:20064375). Binds DNA and mediates the recruitment of the PRC2 complex to target genes in embryonic stem cells, thereby playing a key role in stem cell differentiation and normal embryonic development (PubMed:20064375, PubMed:20075857). In cardiac cells, it is required to repress expression of cyclin-D1 (CCND1) by activating methylation of 'Lys-9' of histone H3 (H3K9me) by the GLP1/EHMT1 and G9a/EHMT2 histone methyltransferases (PubMed:12852854, PubMed:12890668, PubMed:19010785). Also acts as a transcriptional repressor of ANF via its interaction with GATA4 and NKX2-5 (PubMed:15542826). Participates in the negative regulation of cell proliferation signaling (PubMed:10913339). Does not have histone demethylase activity (PubMed:20064376). Associates with the PRC2 complex, which consists of the core components EED, EZH1 or EZH2, SUZ12, and RBBP4, and various combinations of accessory subunits including AEBP2, JARID2, PHF19, MTF2 and EPOP (PubMed:20064376, PubMed:20064375). Found in a monomeric PRC2.2 (class 2) complex consisting of at least SUZ12, RBBP4, AEBP2 and JARID2 (By similarity). Facilitates nucleosome binding of the PRC2 complex (By similarity). Interacts with SUZ12 (via C2H2-type zinc finger domain); the interaction is direct; competes with EPOP for SUZ12 binding (By similarity). Interacts with histone methyltransferases EHMT1/GLP1 and EHMT2/G9a (By similarity). Interacts with GATA4 (via the N-terminal region) (PubMed:15542826). Interacts with NKX2-5 (via the C-terminal region) (PubMed:15542826). Interacts with RB1 (PubMed:15870077). Interacts with ZNF496 (PubMed:17521633). Interacts with ESRRB (PubMed:26523946). Colocalizes with the PRC2 complex on chromatin. Widely expressed in embryos. In adults, expressed at high levels in heart, skeletal muscle, brain and thymus. The ARID domain is required to target the PRC2 complex to its target genes. The GSGFP motif is required for the interaction with SUZ12. Embryos die before 15.5 dpc and show severe cardiac morphological defects and altered heart-specific gene expression. Some, but not all, of the homozygotes develop an abnormal groove in a region just anterior to the midbrain-hindbrain boundary on the neural plate at 8-8.5 dpc and show a defect in neural tube closure in the midbrain region. Variable phenotypes are observed depending on the genetic backgrounds: mutant mice with a C57BL/6J X 129S1/Sv genetic background die upon birth and show cardiac defects such as ventricular septal defects, double-outlet right ventricle, and thin ventricular wall at later embryonic stages. In addition to the thin ventricular wall, mutant embryos with a pure BALB/c background show deficient cell growth in the liver, thymus, and spleen. In contrast, mutant mice with a C3H/He genetic background die at 11.5 dpc, which exhibit hyperplasia and increased cyclin-D1 (CCND1) expression in the trabecular layer of the ventricle at 10.5 dpc. 'Jumonji' means 'cruciform' in Japanese. Belongs to the JARID2 family. Despite the presence of a JmjC domain, lacks the conserved residues that bind the iron cofactor, explaining the absence of histone methyltransferase activity.