tissues are diverse not only in their structure and function but also in the dynamics of their constituent cells ( leblond & walker , 1956 ) . sc turnover rates in adult mouse lineages vary by orders of magnitude ( fig  1 ) .
epithelial and male germ scs cycle rapidly , while in tissues such as liver , kidney and muscle , proliferation is scarcely detectable . in homoeostasis , on average , one sc and one differentiating cell are produced per sc division , and the rate of sc proliferation is matched with the rate of loss of cells from the differentiated lineage(s ) it supports . following damage , however , scs must rapidly and reversibly switch to produce an excess of proliferating cells to regenerate the lost tissue . here
, we will define scs in purely functional terms as cell populations that sustain longterm tissue turnover and/or contribute to tissue repair after injury .
we first survey sc behaviour in high turnover and quiescent tissues in homoeostasis , then consider how scs respond to injury and conclude by considering the physical and molecular signals which switch sc behaviour to meet the requirements of the organism .
there are two cellular mechanisms by which scs may maintain homoeostasis ( watt & hogan , 2000 )
. a population of scs may behave so that on average , 50% of their progeny are themselves scs and 50% differentiating cells .
population asymmetry may result from the cell autonomous properties of scs or external regulation , for example by a niche of restricted size in which scs can only divide when a cell differentiates and leaves the niche .
advances in lineage tracing and live imaging reveal population asymmetry emerges as the predominant mechanism in tissues with a high rate of turnover ( alcolea & jones , 2013 ; rompolas & greco , 2014 ) .
we will focus on tissues in mice where robust evidence on sc behaviour is available , before turning to other species .
some of the first insights into sc dynamics in vivo came from studies of squamous epithelia , which cover the skin , mouth and oesophagus and predominantly consist of layers of keratinocytes .
proliferation is confined to the deepest , basal cell layer , which forms the sc niche ( fig  2a ) .
when dividing cells commit to differentiation , they withdraw from the cell cycle and migrate out of the basal layer ( alcolea & jones , 2014 ) .
largescale lineage tracing has revealed that cellular homoeostasis is achieved by a single population of keratinocyte scs in the basal cell layer ( clayton et  al , 2007 ; doupe et  al , 2010 , 2012 ; mascre et  al , 2012 ; lim et  al , 2013 ) .
the outcome of individual cell divisions is unpredictable , generating two scs , two differentiating cells or one cell of each type ( alcolea & jones , 2013 ) ( fig  2a ) .
however , the probabilities of each division outcome are balanced , so an equal number of scs and differentiating cells are generated across the basal layer , an example of  population asymmetry ( watt & hogan , 2000 ; clayton et  al , 2007 ) .
the random element in sc fate appears at odds with histological features such as the ordered columns of differentiating cells seen in mouse epidermis , but these arise simply from the physical packing properties of suprabasal cells rather than reflecting deterministic sc behaviour ( doupe et  al , 2010 ) .
analysis of lineagetracing data argues that the balanced stochastic fate of squamous scs is a cellintrinsic property rather than a consequence of external regulation , but the molecular machinery that achieves this is unknown ( clayton et  al , 2007 ; jones & simons , 2008 ) .
( a ) squamous epithelia consist of layers of keratinocytes , scs ( green ) reside in the basal cell layer , along with postmitotic cells waiting to stratify ( red ) .
when a differentiating cell leaves the niche ( arrow ) , a nearby sc divides with one of the three division outcomes shown to maintain constant cell density in the niche .
the probabilities of each outcome ( expressed as per cent , oesophageal epithelium shown ) are balanced , so equal numbers of scs and differentiated cells are produced across the population .
( b )  the  hair follicle cycles between a resting stage ( telogen ) and expansion of the lower follicle ( anagen ) .
multiple scs have been identified , in the junctional zone ( purple ) , the bulge ( green ) and the hair germ ( blue ) , which lie in contact with the mesenchymal cells of the dermal papilla ( blue ) .
the hair shaft ( black )  is surrounded by concentric layers  of  inner root sheath cells that have been omitted for clarity . in the transition into anagen , hair germ and upper bulge cells  selfduplicate . in the bulge , divisions are aligned parallel with the axis of the hair shaft ( inset ) .
lower bulge cells contribute differentiating progeny to greatly expand the root sheath . later in anagen
, hair germ cells assemble around the dermal papilla and then generate inner root sheath cells ( arrows ) .
selfrenewal and  differentiation are balanced , so the numbers of scs in each compartment is maintained at a constant level across multiple hair cycles .
( c ) intestinal epithelium contains four lineages sustained by scs ( green ) that lie between paneth cells in the crypt base . differentiating cells migrate through a progenitor compartment in the  upper crypt from which postmitotic cells populate the villus , from which they  are shed .
inset shows a simplified topdown view of the niche . as a differentiating  sc  exits the niche ,
dormant scs ( green ) lie close to arterioles , receiving paracrine signals from endothelial cells ( red ) , perivascular cells expressing ng2 and sympathetic nerve  endings ( blue ) . on activation ,
transplantation of daughter cells of a single sc reveals selfduplicating and asymmetric divisions : dark green : longtermreconstituting scs ; light  green : short or intermediatetermreconstituting scs ; yellow : megakaryocyte progenitor ; and blue : common myeloid progenitor .
lineage tracing in homoeostasis suggests that myeloid lineages may be maintained by selfsustaining progenitor cells ( yellow ) exhibiting  population asymmetry by generating  equal proportions of progenitor and differentiating cells ( grey ) ( see inset ) .
haematopoietic scs ( green ) make negligible contribution to myelopoiesis in homoeostasis , but function as  reserve cells .
( g ) male germ cell scs  are diverse in appearance but functionally equivalent .
male germ cells expressing gfr1 reside in the  outermost layer of the seminiferous tubule .
scs ( green ) exist as singles or 24 cell syncytia  connected by cytoplasmic bridges , which may selfduplicate ( blue arrows )  to generate two scs or undergo fragmentation ( short red arrows ) . upon differentiation ( pink arrow ) into  ngn3positive cells  ( red ) , the same behaviour continues , but ngn3 cells are unlikely to revert to gfr1 
 scs in homoeostasis .
once in the ngn3 compartment , syncytia larger than 4 cells form which may undergo further differentiation into ckitexpressing cells ( not shown ) , which are even less likely to revert to gfr1positive cells .
quiescent neural scs ( light green ) reside in the subventricular zone niche , extending processes into  cerebrospinal fluid ( blue ) that fills the lateral ventricles  ( lv ) and underlying endothelial cells ( red ) lining blood vessels ( bv ) .
cells  ( pink ) and neural precursor cells ( orange ) lie adjacent to the scs .
( i ) division outcomes of neural scs in the dentate gyrus inferred from lineage tracing .
neural scs interconvert between quiescent ( light green ) and  proliferating ( dark green ) states .
division of scs has a range of symmetric and asymmetric outcomes as shown , generating neural scs , neuroblasts ( orange ) or differentiated astrocytes ( blue ) .
the epidermis is punctuated by appendages in the form of hair follicles ( hfs ) and sweat ducts , each a selfmaintaining miniorgan containing multiple cell lineages ( schepeler et  al , 2014 ) .
hfs are split into functionally discrete compartments ( page et  al , 2013 ) .
the lower hair follicle undergoes cyclical expansion ( anagen ) and contraction ( catagen ) followed by a period of quiescence ( telogen ) ( fig  2b ) .
the hf is homoeostatic in sc numbers , and tissue organisation remains the same at telogen phase of each successive hair cycle .
hfs are sustained by sc populations in a region known as the bulge and the adjacent hair germ ( rompolas & greco , 2014 ) .
lineage tracing and cell culture studies have revealed a bewildering range of apparently overlapping candidate scs in hfs , though it is unclear whether variations in gene expression mark functionally distinct sc populations ( rompolas & greco , 2014 ; schepeler et  al , 2014 ) .
the hf bulge , which marks the upper limit of the lower follicle , was first identified as a distinct sc niche as it contains slowcycling cells ( cotsarelis et  al , 1990 ; tumbar et  al , 2004 ) ( fig  2b ) .
bulge scs differentiate into multiple lineages when sorted and transplanted , and undergo both symmetric and asymmetric divisions ( blanpain et  al , 2004 ; waghmare et  al , 2008 ; zhang et  al , 2009 ) .
more recently , lineage tracing and intravital imaging have shown that scs in the hair germ are the first cells to be mobilised as hfs enter anagen , undergoing apparently symmetric selfduplicating divisions aligned with the long axis of the hf ( greco et  al , 2009 ; rompolas et  al , 2012 ) .
only when the exponentially expanding hair germ has morphed to envelop a bud of mesenchyme called the dermal papilla ( dp ) scs differentiate into 
transit amplifying cells that will form the inner root sheath that surrounds the hair shaft ( rompolas et  al , 2012 ) .
signals from the dp are essential for the progression of the hair cycle ; indeed , the number of cells in the dp determines hair size and shape ( rompolas et  al , 2012 ; chi et  al , 2013 ) . in the bulge ,
scs remain in slow cycling or quiescent , until a proportion of cells are recruited into division by signals from ta cells .
these induce scs to first contribute to the outer root sheath and then undergo selfrenewal until the bulge is repopulated with scs , when quiescence resumes ( hsu et  al , 2014 ) ( fig  2b ) .
hf expansion is followed by involution ( catagen ) , and by the time the telogen phase is reached , bulge and hair germ scs are restored , achieving homoeostasis over the entire cycle ( hsu et  al , 2014 ) .
the glandular epithelium that lines the intestine is also rapidly turned over but has a distinctive tissue organisation that contributes to sc regulation .
cell replacement is achieved by scs and progenitor cells located in pits known as crypts ( clevers , 2013 ) ( fig  2c ) .
cycling scs lie at the crypt base among cells expressing the wnt target gene lgr5 , maintaining four lineages of differentiated cells via the lineagecommitted progenitor cells that populate the upper crypt ( barker et  al , 2007 ) .
differentiated paneth cells lie next to scs and secrete signals to sustain scs in the niche ( sato et  al , 2011b ) .
the requirement for paracrine signals restricts the size of the sc pool and ensures homoeostasis .
lineage tracing indicates that as a sc differentiates , it migrates out of the niche and is replaced by the selfduplicating division of a neighbouring sc ( fig  2c ) ( lopezgarcia et  al , 2010 ; snippert et  al , 2010 ) .
it was initially thought that all lgr5 cells were cycling functionally equivalent scs , but a recent study has shown only 5 of the 1415 lgr5 cells in each crypt base are proliferating at any one time ( kozar et  al , 2013 ) .
live imaging further suggests the likelihood of a sc differentiation depends on its location , increasing in the uppermost part of the niche ( ritsma et  al , 2014 ) .
analysis of spontaneous clones carrying mitochondrial mutations argues similar sc behaviour maintains human colonic epithelium ( baker et  al , 2014 ) .
intestinal homoeostasis is thus achieved by linking differentiation to selfduplicating sc division within a niche of restricted size .
it has long been argued that the prodigious cell turnover of the haematopoietic system is sustained by rare scs , found both in the circulation and in a specific niche environment in the bone marrow .
heamopoietic scs ( hscs ) are assayed by their ability to reconstitute the blood system in the long term following transplantation into irradiated host animals ( babovic & eaves , 2014 ; ema et  al , 2014 ) .
highly purified hscs expressing cell surface identical markers may be cycling or dormant , but only the latter group has longterm transplant potential ( fig  1 ) ( wilson et  al , 2008 ; foudi et  al , 2009 ; catlin et  al , 2011 ; anjosafonso et  al , 2013 ; oguro et  al , 2013 ) .
dormant hscs reside in a distinct niche environment , next to arterioles , and migrate to lie close to venous sinusoids on activation ( fig  2d ) ( kunisaki et  al , 2013 ; mendelson & frenette , 2014 ) .
transplant assays argue that haematopoiesis is a hierarchy , with hscs continually generating progenitors that become progressively restricted in both lineage and selfrenewal potentials as they differentiate , but recent discoveries are challenging this view .
transplantation of daughters from a single hsc division reveals selfduplicating and asymmetric divisions which generate a variety of differentiating progenitors directly from hscs , challenging the view of an ordered differentiation programme ( yamamoto et  al , 2013 ) ( fig  2e ) .
more remains to be discovered about the apparent heterogeneity among hscs with longterm transplant potential .
some of this may result from hscs commuting between different states that vary in their ability to survive the rigours of transplantation ( ema et  al , 2014 ; van galen et  al , 2014 ) .
recently , transposonbased lineage tracing has revealed native haematopoiesis is very different from that in transplanted animals . rather than myeloid lineages deriving from a few hscs , as is seen after transplantation , numerous shortlived progenitor clones are observed , consistent with myelopoiesis being maintained by a selfsustaining progenitor pool exhibiting population asymmetry ( fig  2f ) ( sun et  al , 2014b )
this argues for a separation of roles in haemopoiesis , with a pool of progenitors maintaining the myeloid lineage in homoeostasis and quiescent hscs functioning as a 
reserve , mobilised to expand the progenitor population when the demand for myeloid cells rises ( wilson et  al , 2008 ; sun et  al , 2014b ) .
spermatogenesis continues throughout life , sustained by a population of scs , which reside in the basal cell layer of the seminiferous tubule , express gfr1 and are negative for the differentiation marker ngn3 .
spermatogonia undergo incomplete cell division , generating syncytial clusters of cells linked by cytoplasmic bridges ( yoshida , 2012 ) ( fig  2 g ) .
it was thought that only single gfr1 cells were scs , but combined live imaging and lineage tracing have revealed that all gfr1  cells , whether single or in syncytia of up to 4 cells , are functionally equivalent scs ( hara et  al , 2014 ) .
quantitative modelling argues scs divide symmetrically producing two sc daughters , while the stochastic differentiation of a sc into a ngn3 cell appears linked to syncytial fragmentation by an as yet unknown mechanism . in combination , these mechanisms achieve population asymmetry as sc division is balanced with differentiation across the gfr1  compartment ( klein et  al , 2010 ; hara et  al , 2014 ) .
ngn3 cells have a high probability of undergoing differentiation into ckitexpressing cells , but infrequently revert back to gfr1 sc .
the spermatogenesis paradigm supports the concept that sc function may reside in a pool of heterogeneous cells which interconvert between different states , so that there are multiple reversible paths by which a given sc may differentiate ( nakagawa et  al , 2010)(hara et  al , 2014 ) . turning to tissues with a low rate of turnover
, it is now clear that both rodent and human brains , once thought to be postmitotic , continue to produce new neurons throughout life which contribute to specific forms of learning and memory and responding to stress ( snyder et  al , 2011 ; spalding et  al , 2013 ; aimone et  al , 2014 ; ernst et  al , 2014 ) .
adult neural scs are found in the subventricular zone ( svz ) lining the lateral ventricles and in the dentate gyrus ( dg ) of the hippocampus and are largely quiescent ( fig  2h ) .
lineage tracing in transgenic mice reveals that proliferating dg scs are capable of both asymmetric and symmetric divisions generating two scs or two differentiating astroglial or neural progenitor daughters ( bonaguidi et  al , 2011 ) ( fig  2i ) .
after division , some scs return to a quiescent state , negative for proliferation markers , paralleling the transition between dormant and active states seen in heamatopoietic scs . even establishing the existence of scs in adult tissues with a very low rate of turnover
studies in mouse and human support a slow rate of turnover of differentiated hepatocytes in the liver and glomerular and tubular cells in the kidney , though the existence of a discrete stem cell population in these tissues is controversial ( magami et  al , 2002 ; rodins et  al , 2002 ; fellous et  al , 2009 ; kusaba et  al , 2014 ; miyajima et  al , 2014 ) .
in contrast , adult skeletal muscle contains a welldefined quiescent sc population , residing among the satellite cells that lie beneath the plasma membrane of terminally differentiated multinucleate muscle fibres ( brack & rando , 2012 ) .
reserve role of scs , actively maintained in a quiescent state until they are mobilised following muscle injury ( cheung et  al , 2012 ; cheung & rando , 2013 ) . in summary , there are two cellular mechanisms of population asymmetry in mammalian tissues with a high turnover ( watt & hogan , 2000 ; klein & simons , 2011 ) .
open plan niche with an apparently cellintrinsic mechanism which balances the probabilities of generating scs or differentiating progeny ( clayton et  al , 2007 ; alcolea & jones , 2014 ) .
an alternative strategy seen in the intestine is having a niche of limited size in which selfduplicating sc division occurs as a differentiating cell exits the niche ( lopezgarcia et  al , 2010 ; vermeulen & snippert , 2014 ) . in both these examples , the robust linkage of division and the exit of a nearby cell
another common theme is that while the fate of an individual sc is unpredictable , homoeostasis is achieved across the sc population .
the male germ cell lineage illustrates the unreliability of using marker gene expression or cellular morphology to define scs , as such characteristics may vary within a functionally equivalent pool of scs .
likewise , active scs may coexist with those within a dormant state in the hair follicle , bone marrow and intestinal crypt .
while the discussion above has focussed on mammalian systems , population asymmetry has also been observed in drosophila , where neutral competition for a niche of fixed size is seen in ovarian scs , while a balanced three way division outcome reminiscent of mammalian squamous epithelia is a feature of midgut scs ( de navascues et  al , 2012 ; kronen et  al , 2014 ) .
intriguingly transgenic lineage tracing reveals that neural retina scs of the medaka fish , orizias latipes , have fixed asymmetric cell division in homoeostasis , the first observation of such behaviour in an adult tissue ( centanin et  al , 2014 ) . in summary , for the mammalian and drosophila lineages where sc dynamics has been resolved , cellular homoeostasis is achieved by population asymmetry , which may be cell intrinsic or niche specified .
the fate of individual cells is unpredictable , but the probabilities of selfrenewal and differentiation are balanced across the sc population , so equal proportions of scs and differentiating cells are generated .
evolution has also sampled another mechanism of tissue maintenance , fixed asymmetric sc division , but to date , this has only been observed in fish retina .
tissue injury is an inevitable part of life . it is becoming clear that following damage , scs and their differentiating progeny exhibit hitherto unexpected plasticity in their behaviour ( doupe & jones , 2013 ) .
we first consider how cycling sc populations respond to injury before turning to the activation of quiescent scs in low turnover tissues .
wounding is frequent in surface epithelia . in the squamous epithelium of the oesophagus and the epidermis of the paw , scs adjacent to a wound
rapidly and reversibly switch to producing an excess of scs , reverting to homoeostatic behaviour once the defect is closed ( fig  3a ) ( doupe et  al , 2012 ; lim et  al , 2013 ) .
the need for such flexibility may be one of the reasons for three division outcomes in squamous epithelial scs .
pure asymmetric division achieves cellular homoeostasis but is inflexible , while adjusting the probability of the two types of symmetric division allows rapid modulation of cell production .
next to the wound ( w ) exit the cell cycle and migrate towards the defect ( yellow area and  inset ) . behind this  migrating front , cycling progenitors undergo divisions heavily biased to selfduplication ( green area and inset ) , expanding the progenitor compartment to generate the excess cells required to repair the epithelium . once the wound has closed , progenitor behaviour switches back to homoeostasis .
( b ) wound repair in epidermis . in the epidermis , progenitor cells change their behaviour as in the oesophagus , but wound repair is supported by a flux of cells into the epidermis from  hair follicles ( purple arrows ) and , in tail skin , mobilisation of quiescent reserve cells in the epidermis .
migration explains the appearance of radial clones around a healed wound seen in lineagetracing experiments .
following ablation of scs in the bulge ( green ) of telogen hfs , cells in the upper follicle ( purple ) migrate and proliferate ( purple arrows ) to reconstitute the bulge sc population , enabling the hair cycle to proceed normally .
following ablation of lgr5expressing scs in the crypt base ( green ) , paneth cell precursors ( blue with pink border ) dedifferentiate and colonise the crypt base niche with scs functionally equivalent to the original population .
( e ) injury response of male germ scs . following treatment with the cytotoxic agent busulphan ,
the gfr1 
 sc population is depleted ( grey outlines ) but then reconstituted by surviving ngn3 cells reverting into gfr1 cells ( green arrows ) and a decrease in the probability of gfr1 cells transferring to the ngn3 compartment ( pink dotted arrows ) .
dormant scs are recruited into  cycle by treatment after damage to the haematopoietic system from a cytotoxic drug ( 5fu ) or cytokines , such as gcsf , released after infection .
( g ) neural sc responses to stroke . following a cns stroke , which results in cell death due to ischaemia ,
lineage tracing argues these derive both from mobilisation of neural scs in the svc followed by migration to the site of injury ( orange with green border ) and from differentiated astrocytes within the area of the stroke entering a neurogenic programme ( orange with red borders ) .
most of the epidermis has a dense array of hfs , which normally make negligible contribution to homoeostasis . following injury , however , the progeny of bulge and upper follicle stem cells migrate into the epidermis and contribute extensively to wound repair ( ito et  al , 2005 ; levy et  al , 2005 ; page et  al , 2013 ) ( fig  3b ) . in the specialised tail epidermis , which is sparse in hfs , rare ,
reserve scs are mobilised , while in hairless skin , sweat ductderived cells contribute to wound healing ( lu et  al , 2012 ; mascre et  al , 2012 ; roshan & jones , 2012 ) . in humans , similar principles apply , but sweat ducts make a larger contribution to epidermal repair than hfs ( rittie et  al , 2013 ) .
the infiltration of specialised gamma delta t cells following epidermal injury activates wnt signalling via fgf9 signalling ( gay et  al , 2013 ) .
wnt has been shown to alter the axis of division of bulge stem cells to generate a new hair follicle alongside an existing one ( deschene et  al , 2014 ) .
recent developments in live imaging combined with laser ablation to delete cell subpopulations have also revealed unexpected plasticity in hfs .
following ablation , bulge scs are replaced by the progeny from cells in the upper hf which normally make no contribution to the hair cycle ( fig  3c ; rompolas et  al , 2013 ; rompolas & greco , 2014 ) .
only destruction of the niche cells surrounding the bulge or separation of the dp from the hair germ halts hair regeneration , indicating the niche plays an essential role in hair regeneration .
following ablation of the lgr5positive cells in the intestinal crypt , differentiating lineagecommitted precursor cells above the crypt base dedifferentiate into functional scs which repopulate the crypt ( fig  3d ) ( van es et  al , 2012 ; buczacki et  al , 2013 ; ritsma et  al , 2014 ) . in lung and gastric epithelia ,
reversion of postmitotic differentiated cells into scs is observed following injury ( stange et  al , 2013 ; tata et  al , 2013 ) . in nonepithelial tissues , evidence for dedifferentiation
is more limited , but following cytotoxic drug treatment , the depleted male germ cell gfr1  sc pool is regenerated by the combination of decreasing the probability of reversion of gfr1  differentiation and reversion of ngn3 cells , most of which differentiate in homoeostasis , back into gfr1  scs ( fig  3e ; nakagawa et  al , 2010)(hara et  al , 2014 ) .
tissue damage or stress mobilises slowcycling or quiescent scs , which function as  reserve cells , such as dormant haematopoietic scs that are rapidly recruited into cycle following treatment with the cytotoxic drug 5 fluorouracil or the cytokine gcsf , the latter also triggering sc migration into the circulation ( wilson et  al , 2008 ; cheung & rando , 2013 ) ( fig  3f ) .
the liver is an intriguing organ , capable of extensive regeneration after a variety of insults ( miyajima et  al , 2014 ) .
lineage tracing in different models of injury indicates surviving hepatocytes reenter the cell cycle to restore their own lineage ( schaub et  al , 2014 ; tarlow et  al , 2014 ; yanger et  al , 2014 ) .
tissue repair can thus be achieved by dedifferentiation alone in the absence of a reserve stem cell population .
following vascular stroke in mouse brain , lineage tracing provides evidence for differentiated astrocytes generating proliferating neuroblasts , supplementing neuroblasts derived from mobilised neural scs in the svz which have migrated into the zone of injury ( magnusson et  al , 2014 ) ( fig  3 g ) .
the ultimate test of the regenerative potential of a sc is to reconstitute a tissue from a single cell , a feat that requires an exponential increase in sc number and the generation of differentiated cells .
transplantation into immunesuppressed mice has long been a standard sc assay , but more recently , sc culture methods have been developed which reveal the ability of a single sc to reconstitute a tissuelike  organoid in defined culture conditions ( sato et  al , 2009 ; sato & clevers , 2013 ) .
this was first demonstrated with human epidermal scs that generate large colonies containing multiple scs and differentiating keratinocytes , which fuse into stratified sheets ( rheinwald & green , 1975 ; jones et  al , 1995 ) .
when this cultured epidermis is grafted back onto burnt patients , it persists over many years ( gallico et  al , 1984 ; compton et  al , 1989 ) .
more recently , 3dimensional culture systems were established for intestinal and prostatic scs from both mice and humans ( sato et  al , 2009 , 2011a ; chua et  al , 2014 ; karthaus et  al , 2014 ) .
disaggregation and reculturing reveal each organoid contains selfrenewing scs capable of multiple rounds of organoid formation ( sato et  al , 2009 ) .
the ability of scs and their progeny to assemble themselves into a niche within a tissuelike array of differentiated cells in the absence of external spatial cues is remarkable and is most graphically illustrated in the formation of complex brainlike structures in 3d cell culture ( lancaster et  al , 2013 ; lancaster & knoblich , 2014 ) .
if this technology can be used to expand sc populations ex vivo which successfully reconstitute and sustain damaged tissues in vivo , it will have great potential for regenerative medicine ( huch et  al , 2013a , b ; sato & clevers , 2013 ; dorrell et  al , 2014 ) . in combination with genome editing
, ex vivo stem cell expansion may be particularly powerful for treating genetic diseases with tissuerestricted phenotypes , where engrafted scs can compete with host scs on at least even terms ( schwank et  al , 2013 ) .
the factors required to culture organoids give insight into the nature of niche signals for sc survival and proliferation , an area we will explore below ( sato et  al , 2011b ) . to summarise ,
advances in cell culture are further revealing the selforganising ability of scs and their progeny in generating organlike structures in the absence of tissue cues .
we now turn to examine recent insights into the regulation of sc dynamics in homoeostasis and regeneration , critical in tuning cell production to the requirements of the tissue and whole organism .
potentially adjustable parameters include the rate of sc division and the balance of the resulting sc and differentiating progeny . in tissues with minimal cell turnover , scs
we will consider the relative contributions of cellintrinsic factors , paracrine signalling in the sc microenvironment , the physical characteristics of the niche and 
remote signals such as hormones and neural regulation in switching sc behaviour . for squamous scs
, population asymmetry requires balancing the probabilities of three potential division outcomes ( clayton et  al , 2007 ; doupe et  al , 2012 ) .
this process requires notch signalling , which was long known to drive the differentiation of postmitotic keratinocytes ( lowell et  al , 2000 ; rangarajan et  al , 2001 ; nicolas et  al , 2003 ; blanpain et  al , 2006 ) .
transgenic inhibition of notch signalling in individual oesophageal scs accelerates the rate of cell division and blocks the symmetric differentiation division outcome ( alcolea et  al , 2014 ) . as a result ,
intriguingly , as this occurs , the basal layer becomes crowded and the symmetric differentiation division outcome is restored ( alcolea et  al , 2014 ) . in culture
, cell crowding promotes keratinocyte differentiation , suggesting the reinstatement of homoeostasis may be a consequence of increased cell density within the basal layer ( watt et  al , 1988 ) .
regulation of cell density is a robust and widespread phenomenon , and potentially is a defence against scs carrying any mutation that enhances proliferation and results in crowding in the niche ( eisenhoffer et  al , 2012 ; marinari et  al , 2012 ; frede et  al , 2014 ) .
the regulation of squamous sc proliferation also involves highly conserved cell  cell and paracrine signalling pathways .
epidermal scs secrete both wnt ligands and wnt inhibitory dkk proteins , resulting in the activation of wnt target genes in basal cells ( choi et  al , 2013 ; lim et  al , 2013 ) .
blockade of wnt signalling in scs inhibits their proliferation , resulting in a thinned epidermis ( choi et  al , 2013 ; lim et  al , 2013 ) .
autocrine wnt signalling is thus an essential part of the squamous sc niche , providing permission to proliferate ( frede & jones , 2013 ) .
the remodelling of hfs during the hair cycle makes dissection of sc regulation in the fastchanging niche especially challenging , but cell autonomous factors and paracrine signalling again emerge as crucial sc regulators .
expression of the transcription factor sox9 in hf scs is essential for their survival and normal differentiation , but this is achieved at least in part by regulation of paracrine activin / tgf signalling by sox9 target genes ( kadaja et  al , 2014 ) .
if wnt signals are inhibited , hf scs enter a state of  suspended animation in which they persist long term but do not proliferate , reentering the cell cycle when the wnt activity is reinstated ( choi et  al , 2013 ) .
in contrast , activating the wnt pathway triggers sc expansion and tilts the axis of cell division to generate new hfs ( deschene et  al , 2014 ) . as with the epidermis , there is evidence for paracrine signalling , as scs with high wnt activity recruit adjacent scs by secreting wnt ligands ( deschene et  al , 2014 ) .
hedgehog signalling mediates the activation of quiescent scs by differentiating ta cells ( hsu et  al , 2014 ) .
the short range of wnt signals from paneth cells , essential for scs remaining in an undifferentiated state , restricts the number of scs in the intestinal niche ( sato et  al , 2011b ) .
expansion of the paneth cell population is a feature of benign intestinal tumours , whose formation is driven by wntactivating apc mutations ( schepers et  al , 2012 ) .
apcmutant scs eventually colonise the crypt through their enhanced fitness over wildtype cells , as a differentiating cell is more likely to be replaced by a mutant than a wildtype cell ( vermeulen et  al , 2013 ) .
loss of lrig1 , which negatively regulates erbb family growth factor signalling , causes crypt expansion , while activation of ras , which lies downstream of erbb receptors , in intestinal scs can trigger a process called crypt fission in which a mutant crypt splits into two allowing a mutant stem cell clone to spread through the intestine ( wong et  al , 2012 ; amoyel et  al , 2014 ) .
thus , while limiting niche size is a simple means of achieving homoeostasis , it is not invulnerable to mutations that confer a clonal fitness advantage on scs .
the morphology of the niche has long been recognised as of pivotal importance in plants , whose architecture is determined by the spatial arrangement of the meristem ( heidstra & sabatini , 2014 ) .
the size and shape of hair can be manipulated by altering the number of cells in the dermal papilla that forms the niche for hair germ scs ( chi et  al , 2013 ) . within the bone marrow ,
hscs reside in close proximity to stromal cells adjacent to blood vessels and the bone surface ( mendelson & frenette , 2014 ) .
each of these cell types makes a distinct paracrine contribution to the niche ( ding et  al , 2012 ) .
for example , the chemokine cxcl12 , which is essential for maintaining hscs , derives primarily from the perivascular stromal cells that lie directly adjacent to quiescent hscs ( ding & morrison , 2013 ; greenbaum et  al , 2013 ) .
paracrine niche signals also regulate neural scs in the svz , which extend cellular processes into the cerebrospinal fluid ( csf ) that fills the ventricles and forms contacts with underlying endothelial cells ( fig  2h ) ( silvavargas et  al , 2013 ; codega et  al , 2014 ) .
these contacts allow regulation of neural scs via both secreted factors in the csf and signals from the vasculature .
for example , endotheliumderived ntf3 and g proteincoupled receptor ligands in the csf promote sc quiescence ( codega et  al , 2014 ; delgado et  al , 2014 ) .
seemingly at odds with scs residing in an ordered niche is their ability to recapitulate the morphology of a tissue in culture ( rheinwald & green , 1975 ; sato et  al , 2009 ; stange et  al , 2013 ; karthaus et  al , 2014 ) . feeder cells or exogenous growth factors and ligands in the media are able to substitute for the paracrine environment provided by the niche , but in isotropic 3dimensional culture systems , morphogenic gradients are initially absent .
a common feature of many protocols is the requirement for the rock kinase inhibitor y26732 during establishment of the culture .
this suggests that manipulation of cytoskeletal signalling is required for isolated scs to enter a state that allows survival and promotes proliferation in the absence of niche cells ( sato et  al , 2009 ; huch et  al , 2013a , b ; karthaus et  al , 2014 ) . rather than being determined by scs , the resemblance of organoids to their parent tissue may rest on the ability of differentiating cells to selfassemble into a tissuelike array by virtue of cell shapedefined packing considerations and differential adhesion ( watt & green , 1982 ; honda et  al , 1996 ) .
thus , recent studies are revealing more of the microarchitecture of the sc niche and the highly conserved paracrine signals , such as wnt , which regulate cell behaviour across a wide range of lineages . while the niche may not 
micromanage the outcome of each individual sc division , it has an essential role in sustaining sc populations in a proliferating or quiescent state .
understanding how cellintrinsic factors , autocrine signals and exogenous factors combine to sustain scs in culture will likely give new understanding of the niche in vivo .
stem cell behaviour must not only match local requirements in the tissue , but also needs across the organism ( fig  4 ) .
for example in the mouse oesophagus , 10fold more scs undergo mitosis in the early diurnal than in the early nocturnal phase ( burns et  al , 1976 ) . in the epidermis ,
hair follicle bulge scs vary in their transcription of the per1 gene , arguing they are in different phases of the circadian cycle .
cells high in per1 expression have increased clonogenicity in vitro , suggesting variation in circadian phase may contribute to functional heterogeneity in bulge scs ( janich et  al , 2011 ) . in the hematopoietic system ,
scs regularly leave the bone marrow and enter the circulation before returning to their niche .
this migration also has a circadian rhythm with twice as many circulating scs in the diurnal than in the nocturnal phase .
the exit of scs is controlled centrally from the suprachiasmatic nucleus in the brain , via release of noradrenaline from nerve endings in the bone marrow , which in turn regulates the transcription of cxcl12 , a chemokine that directs hsc migration ( mendezferrer et  al , 2008 ) .
sex hormone regulation of reproductive and mammary scs is well documented , but recently has been found to extend to scs in other tissues .
for example , hscs are subject to positive regulation of proliferation and selfrenewing cell divisions by oestrogen in female mice . in pregnancy ,
oestrogen levels rise , the number of cycling hscs increases and more erythroid progenitor cells are produced , meeting the physiological requirement of the animal for increased oxygen delivery to tissues ( nakada et  al , 2014 ) .
another example is the hair cycle , which is arrested during in pregnancy by prolactin driving hf scs into a quiescent state ( goldstein et  al , 2014 ) .
a significant evolutionary pressure on organisms and scs is starvation , which induces a bodywide adaptive response that includes effects on scs ( longo & mattson , 2014 ; mihaylova et  al , 2014 ) .
the midgut of fasted drosophila expands dramatically after feeding , underpinned by a switch in the mode of sc division from balanced cell production to selfduplication in response to insulin ( o'brien et  al , 2011 ) . in the murine small intestine
, fasting reduces mtorc1 signalling in the paneth cells that form the sc niche ( yilmaz et  al , 2012 ) . in turn , this increases paracrine signalling to scs via cyclic adp ribose , resulting in an increased efficiency of organoid formation in cultures from fasted animals ( yilmaz et  al , 2012 ) . while not definitive , this result suggests starvation may expand the sc population by acting on the niche .
starvation also impacts haematopoiesis , acting via igf1 signalling to increase the number of transplantable hscs consistent with an enhanced probability of selfrenewing division ( cheng et  al , 2014 ) .
another route for physiological sc regulation is via the nervous system , recently revealed as having a key role in hsc regulation .
chronic psychological stress induces increased levels of leucocytes . as with circadian control , this effect is mediated by noradrenaline release from sympathetic neurons in the bone marrow , which decreases production of cxcl12 in niche cells triggering hsc proliferation ( heidt et  al , 2014 ) .
the importance of this mechanism is illustrated in the neoplastic myeloproliferative disorder , which is caused by jak2 mutations in hscs ( arranz et  al , 2014 ) .
secretion of interleukin 1b by the mutant hscs induces neuropathy in bone marrow , decreasing cxcl12 levels and triggering hsc proliferation and disease progression .
the development of the disease is halted by restoring adrenergic signalling by treatment with 3adrenergic agonists ( arranz et  al , 2014 ) .
hscs also illustrate how systemic signals interact with cellintrinsic factors to promote the generation of a specific lineage from a multipotent sc population .
for example , the cytokine mcsf , which is released in high levels during infection , induces the master myeloid transcription factor pu1 , increasing the probability of hscs differentiating into myeloid progenitors to meet the increased requirement for leucocytes ( mossadeghkeller et  al , 2013 ) .
drawing these studies together reveals a new aspect of sc biology that goes beyond single lineage or tissue .
understanding how neural , endocrine and cytokine signals regulate cell production to meet the requirements of an organism is a key challenge for sc research .
maintaining the quiescence of scs is an active process ( cheung & rando , 2013 ) .
for example , muscle satellite cells are maintained in a quiescent state by specific mirnas and transcription factors downstream of notch , loss of which results in depletion of the sc population ( fukada et  al , 2011 ; cheung et  al , 2012 ; crist et  al , 2012 ) . in the liver , the hepatocytes that fulfill the role of 
reserve scs are actively maintained in a quiescent and differentiated state by hippo signalling acting via the notch pathway ( yimlamai et  al , 2014 ) .
entry into cycle may require specific transcription factors , such as ascl1 , which is required for neural scs to exit the quiescent state ( andersen et  al , 2014 ) .
, the rapid upregulation of translation is achieved by posttranslational mechanisms involving the sequestration of regulatory mirnas in mrnp granules ( crist et  al , 2012 ) . following a remote injury , circulating factors acting via hgf signalling and the mtorc1 signalling node prime quiescent scs enhancing their regenerative potential .
once activated , some scs contribute to differentiated muscle , while others reenter the quiescent state to maintain the sc population ( shea et  al , 2010 ) .
return to quiescence requires multiple factors including sprouty1 , a negative regulator of receptor tyrosine kinase signalling and active notch signalling ( shea et  al , 2010 ; gopinath et  al , 2014 ) .
it is becoming clear that the quiescent state is far from being a protected state as used to be thought . while cell competition results in the loss of mutant scs in proliferating tissues , quiescent scs accumulate epigenetic and genetic damage , resulting in impaired function as they age ( liu et  al , 2013 ; martins et  al , 2014 ; sun et  al , 2014a ) .
in quiescent hscs , the errorprone nonhomologous endjoining dna repair alterations progressively accumulate ( mohrin et  al , 2010 ; beerman et  al , 2014 ) .
recruitment of hscs into cycle is accompanied by induction of a broad range of dna repair genes mobilised to remedy genomic alterations ( beerman et  al , 2014 ) . as well as intrinsic factors , ageassociated inflammatory signalling acting via the jak / stat pathway impairs muscle sc function ( price et  al , 2014 ; tierney et  al , 2014 ) .
intriguingly , administration of a single circulating growth factor , gdf11 , seems able to reverse the defects in ageing muscle scs ( sinha et  al , 2014 ) .
gdf11 also benefits neurogenesis by ageing neural scs , possibly acting via effects on the vasculature in the svz ( katsimpardi et  al , 2014 ) .
understanding how quiescent scs accumulate molecular damage and the ways in which this may be reversed is a central question in the biology of ageing .
adult scs have evolved a diverse repertoire of sc behaviours to meet tissuespecific requirements . in cycling tissues ,
homoeostatic balance between selfduplication and differentiation may be achieved by cellintrinsic mechanisms , a spatially constrained niche , or exceptionally invariant asymmetric cell division . in each case ,
sc division is restrained by the requirement to maintain a constant cell density within the niche .
repair is also achieved by diverse strategies , with mobilisation of reserve scs , plasticity of sc behaviour and dedifferentiation emerging as common themes .
while specific growth factors may bias cellintrinsic lineage selection , a shared paracrine signalling toolkit sustains scs across multiple lineages ( clevers et  al , 2014 ) .
the application of powerful imaging and transgenic tools to reveal the dynamics of scs within their niche offers the prospect of integrating molecular and cellular mechanisms to gain a broader perspective on the functional plasticity of scs in the context of the whole organism .
 abstractadult organisms have to adapt to survive , and the same is true for their tissues . rates and types of cell production 
 must be rapidly and reversibly adjusted to meet tissue demands in response to both local and systemic challenges . 
 recent work reveals how stem cell ( sc ) populations meet these requirements by switching between functional states tuned to homoeostasis or regeneration . 
 this plasticity extends to differentiating cells , which are capable of reverting to scs after injury . 
 the concept of the niche , the microenvironment that sustains and regulates stem cells , is broadening , with a new appreciation of the role of physical factors and hormonal signals . here 
 , we review different functions of scs , the cellular mechanisms that underlie them and the signals that bias the fate of scs as they switch between roles . 
Introduction
The functional repertoire of SCs
Regeneration: using all the options
Autonomy and instruction: regulating SC states
Remote control: integrating SC dynamics and whole body physiology
Sleeping, waking and sleeping again: regulating SC quiescence
Conclusion
Conflict of interest