Welcome to Scribd, the world's digital library. Read, publish, and share books and documents. See more
Download
Standard view
Full view
of .
Look up keyword
Like this
1Activity
0 of .
Results for:
No results containing your search query
P. 1
http://www.hotbuzz4u.com/wp-content/uploads/2010/03/camel-spider-image.jpg

http://www.hotbuzz4u.com/wp-content/uploads/2010/03/camel-spider-image.jpg

Ratings: (0)|Views: 9|Likes:
Published by Nora Yücel
Individual cell fate decisions can vary according to changes in gene expression in response to environmental, developmental, or metabolic cues. This plasticity is tightly regulated during embryonic development and mediated by the exquisitely coordinated activation and repression of groups of genes. Genes that become repressed are immersed in a condensed chromatin environment that renders them refractory to stimulation. This mechanism is responsible for both the loss of cell plasticity during differentiation and the preservation of cell identity. Understanding the molecular events involved in the establishment and maintenance of these restrictive domains will benefit the design of strategies for cellular reprogramming, differentiation, and cancer treatment.
Individual cell fate decisions can vary according to changes in gene expression in response to environmental, developmental, or metabolic cues. This plasticity is tightly regulated during embryonic development and mediated by the exquisitely coordinated activation and repression of groups of genes. Genes that become repressed are immersed in a condensed chromatin environment that renders them refractory to stimulation. This mechanism is responsible for both the loss of cell plasticity during differentiation and the preservation of cell identity. Understanding the molecular events involved in the establishment and maintenance of these restrictive domains will benefit the design of strategies for cellular reprogramming, differentiation, and cancer treatment.

More info:

Published by: Nora Yücel on Nov 11, 2010
Copyright:Attribution Non-commercial

Availability:

Read on Scribd mobile: iPhone, iPad and Android.
download as PDF, TXT or read online from Scribd
See more
See less

11/11/2010

pdf

text

original

 
Cell Stem Cell
Perspective
Epigenetic Mechanisms that Regulate Cell Identity 
Marı´aJ. Barrero,
1
Stephanie Boue´ ,
1
and Juan Carlos Izpisu´ a Belmonte
1,2,
*
1
Center of Regenerative Medicine in Barcelona, Dr. Aiguader, 88, 08003 Barcelona, Spain
2
Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA *Correspondence:belmonte@salk.eduorizpisua@cmrb.eu(J.C.I.B.) DOI10.1016/j.stem.2010.10.009
Individualcellfatedecisionscanvaryaccordingtochangesingeneexpressioninresponsetoenvironmental,developmental, or metabolic cues. This plasticity is tightly regulated during embryonic development andmediated by the exquisitely coordinated activation and repression of groups of genes. Genes that becomerepressed are immersed in a condensed chromatin environment that renders them refractory to stimulation.Thismechanismisresponsibleforboththelossofcellplasticityduringdifferentiationandthepreservationof cell identity. Understanding the molecular events involved in the establishment and maintenance of theserestrictivedomainswillbenefitthedesignofstrategiesforcellularreprogramming,differentiation,andcancer treatment.
Despite sharing the same genome, different cell types froma given organism respond differently to environmental, develop-mental, or metabolic cues. This variable property, or plasticity of responsiveness, is a defining aspect of a cell’s identity and ismainly interpreted at the level of gene expression. Stem andprogenitor cells are a special case, given that their potential forplasticity is, by definition, more pronounced than for othertissue-specific cells. During differentiation, stem cells lose theirplasticityandnarrowdowntheiridentityintoaparticulardifferen-tiated cell type. For many years this differentiated state wasthought to be irreversible but recent findings indicate that it ispossible to manipulate cells in order to change cell identity orto regain plasticity. Understanding how fate decisions are regu-lated and maintained by different cell types, both during devel-opment and under pathological or experimental conditions,represents an important step toward the successful manipula-tion of cell plasticity in clinical settings.We have known for a long time that genetic material associ-ateswithstructuralproteinstoconstitutechromatin,whichplaysimportant roles structurally and functionally. Hence, genesimmersed in highly packed areas of chromatin remain largelyinaccessible, fail to recruit the RNA polymerase to their pro-moters, and thus remain silent and refractory to stimulation.However, genes having a more open and accessible chromatinstructure are more likely to recruit and engage the RNA poly-merase into productive rounds of transcription and their expres-sion is more prone to be modulated by signaling events. Impor-tantly, the chromatin environment in which a particular gene isembedded can differ from one cell type to another, contributingto cell diversity and identity.Thefundamentalunitofchromatinisthenucleosome,whichiscomposed of two copies each of four core histones, H2A, H2B,H3,andH4,andwrappedby146bpofDNA.TheN-terminaltailsof histones are relatively accessible to enzymatic modificationssuch as acetylation, methylation, phosphorylation, ubiquitina-tion, and sumoylation. Of all the known histone modifications,acetylation is the only modification that directly causes a struc-tural relaxation of chromatin by introducing a negative charge.Other modifications seem to act as docking sites that promotethe recruitment and stabilization of effector protein complexesrather than altering the chromatin structure per se. In a similarfashion, DNA methylation, which takes place at cytosine resi-dues within CpG dinuclotides at gene promoters, is usuallycorrelated with transcriptional repression and mediates itseffect by blocking the binding of transcription factors and/orfacilitating the assembly of repressor complexes at the methyl-ated regions. In general, the presence of histone modificationsinvolved in gene activation, such as trimethylation of histoneH3 at lysine 4 (H3K4me3), promotes the recruitment andstabilization of effector complexes with histone acetyltransfer-ase (HAT) and ATP-dependent remodeling activities. Thesecomplexes mediate the acetylation of histones and stimulatethe mobility of the nucleosomes, or even their eviction, to facili-tate the relaxation of chromatin. Ultimately, this change rendersDNA more accessible and facilitates the recruitment of DNA-binding transcription factors to target genes, which in turncontribute to the recruitment of RNA polymerase and the stabi-lization of the preinitiation complex (PIC). Modifications involvedin gene repression, such as DNA methylation and trimethylationofhistoneH3atlysine9(H3K9me3)andatlysine27(H3K27me3),serve as docking sites for repressor complexes that containhistone deacetylase (HDAC) and ATP-dependent remodelingactivities. The action of these complexes, together with therecruitmentofstructuralnonhistoneproteins,leadstochromatincompaction and reduced DNA accessibility.
Molecular Basis of Pluripotency in EmbryonicStem Cells
The chromatin in pluripotent embryonic stem cells (ESCs) dis-plays distinctive features when compared to differentiated cells.In ESCs the chromatin structural proteins display hyperdynamicinteractions with chromatin ( Meshorer et al., 2006 ) and the over-all transcriptional activity is hyperactive compared to differenti-ated cells ( Efroni et al., 2008 ). ESCs also express high levels of chromatin-remodeling factors involved in maintaining the openchromatin status. Moreover, variations in the expression levelsof specific subunits of remodeling complexes, such as the BAFcomplex, in ESCs relative to differentiated cells leads to theformation of unique remodeling complexes that differ in subunitcomposition and potentially in function ( Ho et al., 2009 ). These
Cell Stem Cell
, November 5, 2010
ª
2010 Elsevier Inc.
565
 
specialized complexes could contribute to sustain high levels of transcriptional activity in pluripotent cells. This idea is furthersupported by the reported loss of self-renewal caused by thedepletion ofthe remodeling factorsChd1 orBrg1inESCs Efroniet al., 2008; Gaspar-Maia et al., 2009 ).ESCs feature a unique plasticity that allows them to differen-tiate into virtually any cell type of the adult organism. This prop-erty, called pluripotency, relies on the fact that critical genesinvolved in differentiation, despite remaining silent, have apermissive chromatin structure that makes them sensitive todifferentiation-inducing signals. This permissive chromatin envi-ronment is characterized by the presence of large H3K27me3domainsharboringsmallerregionsofH3K4me3aroundthetran-scriptional startsite ofcritical developmental genes.The coexis-tence of these two antagonistic marks is the defining feature of so-called bivalent genes and has been suggested to playa role in silencing differentiation genes in ESCs while keepingthem poised for activation upon initiation of specific develop-mental pathways (  Azuara et al., 2006; Bernstein et al., 2006 ).Moreover, the poised nature of these bivalent domains is furtherreinforced bytheabsence ofDNAmethylation,despite thepres-ence of numerous CpG islands ( Fouse et al., 2008; Meissneret al., 2008 ) and the presence of poised RNA polymerase II atthe transcription initiation site of the marked genes ( Guentheret al., 2007 ). Ultimately, the physiological function of bivalentdomains might be to maintain important regulatory sequencesaccessible and responsive at very early stages of differentiationGargiulo et al., 2009 ). Importantly, genes marked with bivalentdomains often encode master transcription factors that areinduced very early during differentiation, usually in a lineage-restricted manner, and that are able to orchestrate wholeprograms of gene expression in differentiated cells. Although the bivalent marks are faithfully transmitted throughcell division in self-renewing cells, they should not be regardedas static but as the result of a highly dynamic equilibrium thatis controlled by the balance of histone-modifying enzymesrecruited to theseareas. The polycomb group of proteins (PcGs)has been described to play an essential role in maintaining thepluripotent state of ESCs by mediating H3K27 methylation atthe bivalent domainsSurface etal.,2010 ). PcG proteins localizeat genes encoding developmental regulators and correlate withthe presence of H3K27 trimethylation both in mouse and humanESCs. Moreover, mouse ESCs null for specific PcG proteinsexhibit decreased H3K27 methylation and aberrant expressionof key developmental genes ( Boyer et al., 2006; Lee et al.,2006 ). On the other hand, the H3K4me3 marks present at thebivalent domains of silent developmental genes could be cata-lyzed by trithorax (trxG) homologs that belong to the MLL family,althoughtheirputativecontributiontotheestablishmentofthesedomains remains unknown. As part of a highly dynamic andresponsive equilibrium, it is likely that histone lysine demethy-lases also contribute to keep the appropriate balance of marksat these domains. Confirming this idea, is the observation thatthePcGsrecruittheH3K4demethylaseRBP2 toitstargetgenesto maintain the proper balance of H3K4 and H3K27 methylationat the bivalent domains in mouse ESCs ( Pasini et al., 2008 ).To fully understand the role of bivalent domains in ESCs, itis important to know how these domains are first established.Bivalent marks have been reported to exist in pluripotent cellsin the embryo and to appear after fertilization during genomicactivation at the maternal-zygotic transition ( Vastenhouw et al.,2010 ). In addition, recent reports describe the presence of microregions of H3K27me3 at the transcriptional start sites of developmental regulators in sperm. The persistence of thesediscrete regions after fertilization and the presence of CpGislands at the promoters of the marked developmental genesmight serve as primers for the establishment of broadH3K27me3 domains during genome activation in embryosBrykczynska et al., 2010 ). However, it is likely that specific tran-scription factors also contribute to establish and/or maintainthese domains. Indeed, genome-wide correlation studies haverevealed that the self-renewal transcription factors Oct4, Sox2,and Nanog occupy not only promoters of genes involved inself-renewal but also of a high number of genes that containbivalent domains ( Boyer et al., 2005 ), suggesting that they playa role in keeping this genes silenced. In agreement with thismodel, it has been reported that Nanog and Oct4 interact withcomplexes involved in transcriptional repression, includingPcG subunits ( Pardo et al., 2010; Wang et al., 2006 ). Anotherpotentialtranscriptionfactorthatcouldbeinvolvedinthemolec-ular arrangement of these domains is JARID2, which has beenrecently suggested to participate in the recruitment of PcG tothe regulatory regions of target genes in mouse ESCs ( Landeiraet al., 2010; Li et al., 2010; Pasini et al., 2010; Peng et al., 2009 ).
Chromatin Dynamics during Differentiation
The permissive chromatin structure present in multipotent cellsis progressively and selectively closed during differentiation. Accessible regulatory areas, such as bivalent domains, closeup and are no longer accessible to transcription factors, leadingto a loss of regulatory potential ( Gargiulo et al., 2009 ).The analysis of the genome-wide distribution of histone andDNA methylation marks and their correlation with gene expres-sion in ESCs, in vitro differentiated ESCs, and adult cells hasprovided a better understanding of gene plasticity in pluripotentand differentiated tissues Fouse et al., 2008; Hawkins et al.,2010; Meissner et al., 2008; Mikkelsen et al., 2007 ). Thesestudies have led researchers to focus on two types of genes:ones with promoters enriched in CpG islands (HCP) and thoseshowing poor representation of CpGs (LCP) Figure 1 ). HCPgenes are usually devoid of DNA methylation in ESCs andinclude self-renewal and housekeeping genes usually markedwithH3K4me3anddevelopmentalregulatorscontainingbivalentdomains. This pattern suggests that the targets of trxG are pro-tected against DNA methylation and are transcriptionally activeunless actively repressed by PcG proteins ( Mikkelsen et al.,2007 ). LCP genes are not expressed, show DNA methylation,and are mostly devoid of H3K4 or H3K27 methylation in ESCsMeissner et al., 2008 ). These genes are likely to be targets of earlymastertranscriptionfactorsandthustheybecomeinducedlate duringdifferentiation in a tissue-specific manner to carry outspecialized functions in particular tissues.Differentiation to one particular lineage implies the permanentand irreversible silencing of genes involved in alternative line-ages as well as those necessary for pluripotent cells. For exam-ple, pluripotency genes lose H3K4me3 and gain distinct combi-nations of repressive marks (H3K27me3, H3K9me3, and DNA methylation). Bivalent genes that become irreversibly silenced
566
Cell Stem Cell
, November 5, 2010
ª
2010 Elsevier Inc.
Cell Stem Cell
Perspective
 
loseH3K4me3andpreserveH3K27me3Cuietal.,2009;Mikkel-sen et al., 2007 ). Usually, repression is further reinforced by theexpansion of the H3K27 methylated areas or the accumulationof a second repressive mark, such as H3K9me3 or DNA methyl-ation Hawkins et al., 2010 ). This ‘‘double lock’mechanismensures permanent repression of developmental and pluripo-tency genes and thus preserves cell identity.How chromatin modifying and remodeling activities partici-pate in the process of differentiation is not yet fully understood.The switch of signaling events that characterizes the transitionfrom self-renewal to differentiation induces dramatic changesin gene expression, including the downregulation of genesinvolved in self-renewal and changes in the expression of criticalchromatin regulators ( Pardo et al., 2010; Wang et al., 2006 ). Thislast event can lead to variations in the subunit composition of effector complexes, allowing them to carry out specialized func-tions during differentiation. Contrary to previous perceptions, inwhich chromatin marks could be passively diluted, severalreports point out the importance of active and targeted removalof marks. Such is the role of the H3K27 demethylases UTX andJmjd3 in the activation of Hox genes during development (  Aggeret al., 2007 ) and in neuronal commitment ( Burgold et al., 2008 ). Both demethylases associate with MLL complexes, suggestingthat removal of the H3K27me3 mark and maintenance of theH3K4me3 at bivalent genes that become activated during differ-entiation are coordinated events. Less is known about themolecular regulation and physiological relevance of a smallpercentage of bivalent domains that remain unresolved upondifferentiation and that are thus bivalent in adult cells ( Figure 1 ).Perhaps more intriguing is the fact that a few new bivalentregions are established during differentiation ( Mikkelsen et al.,2007 ). Regarding the activities that participate in repressionduring differentiation, the methyltransferase G9a is needed forthe proper silencing of genes, among which are self-renewalfactors such as Oct4 ( Feldman et al., 2006 ). G9a catalyzes themethylation of H3K9 at the regulatory regions of these genesduring differentiation, which in turn facilitates the binding of heterochromatin protein 1 (HP1) and de novo DNA methylation.
Reprogramming and Cell Plasticity
For many years the differentiated state was thought to be irre-versible. However, several experimental strategies have beendeveloped to induce the reactivation of the embryonic programin differentiated cells, a process known as nuclear reprogram-ming. Historically, nuclear transfer experiments showed thatthe genetic content of adult and embryonic cells is equivalent
Figure 1. Epigenetic Map of Fate
Genome-wide and correlation studies ( Boyer et al., 2005; Doi et al., 2009; Fouse et al., 2008; Hawkins et al., 2010; Meissner et al., 2008; Mikkelsen et al., 2007 )have allowed the classification of genes according to their genetic, epigenetic, and transcriptional status in different cell types and physiological situations. Thisclassification scheme derives from statistical correlations of broad data sets, and thus not all genes will follow the flowchart precisely. Blue arrows denote tran-sitions from self-renewal to differentiation, red arrows denote transitions to cancer, and gray arrows indicate critical changes to regain pluripotency duringreprogramming.ONandOFFrefertotranscriptionalstatus;DNAmereferstoDNAmethylation;OSNtargetsreferstogenesoccupiedbyOct4,Sox2,andNanog;and trimethylation at lysine 4, 9, or 27 of histone H3 is referred to as H3K4me3, H3K27me3, and H3K9me3, respectively. Marks separated by a slash indicateco-occurrence of marks.
Cell Stem Cell
, November 5, 2010
ª
2010 Elsevier Inc.
567
Cell Stem Cell
Perspective

You're Reading a Free Preview

Download
scribd
/*********** DO NOT ALTER ANYTHING BELOW THIS LINE ! ************/ var s_code=s.t();if(s_code)document.write(s_code)//-->