Cell Reprogramming Requires Silencing of a Core Subset of Polycomb Targets

English version České info

Transcription factor (TF)–induced reprogramming of somatic cells into induced pluripotent stem cells (iPSC) is associated with genome-wide changes in chromatin modifications. Polycomb-mediated histone H3 lysine-27 trimethylation (H3K27me3) has been proposed as a defining mark that distinguishes the somatic from the iPSC epigenome. Here, we dissected the functional role of H3K27me3 in TF–induced reprogramming through the inactivation of the H3K27 methylase EZH2 at the onset of reprogramming. Our results demonstrate that surprisingly the establishment of functional iPSC proceeds despite global loss of H3K27me3. iPSC lacking EZH2 efficiently silenced the somatic transcriptome and differentiated into tissues derived from the three germ layers. Remarkably, the genome-wide analysis of H3K27me3 in Ezh2 mutant iPSC cells revealed the retention of this mark on a highly selected group of Polycomb targets enriched for developmental regulators controlling the expression of lineage specific genes. Erasure of H3K27me3 from these targets led to a striking impairment in TF–induced reprogramming. These results indicate that PRC2-mediated H3K27 trimethylation is required on a highly selective core of Polycomb targets whose repression enables TF–dependent cell reprogramming.

Vyšlo v časopise: Cell Reprogramming Requires Silencing of a Core Subset of Polycomb Targets. PLoS Genet 9(2): e32767. doi:10.1371/journal.pgen.1003292
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1003292

Souhrn

Zdroje

1. DavisRL, WeintraubH, LassarAB (1987) Expression of a single transfected cDNA converts fibroblasts to myoblasts. Cell 51: 987–1000.

2. TakahashiK, YamanakaS (2006) Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126: 663–676.

3. PlathK, LowryWE (2011) Progress in understanding reprogramming to the induced pluripotent state. Nat Rev Genet 12: 253–265.

4. LiR, LiangJ, NiS, ZhouT, QingX, et al. (2010) A mesenchymal-to-epithelial transition initiates and is required for the nuclear reprogramming of mouse fibroblasts. Cell Stem Cell 7: 51–63.

5. Samavarchi-TehraniP, GolipourA, DavidL, SungHK, BeyerTA, et al. (2010) Functional genomics reveals a BMP-driven mesenchymal-to-epithelial transition in the initiation of somatic cell reprogramming. Cell Stem Cell 7: 64–77.

6. BanitoA, RashidST, AcostaJC, LiS, PereiraCF, et al. (2009) Senescence impairs successful reprogramming to pluripotent stem cells. Genes Dev 23: 2134–2139.

7. HongH, TakahashiK, IchisakaT, AoiT, KanagawaO, et al. (2009) Suppression of induced pluripotent stem cell generation by the p53–p21 pathway. Nature 460: 1132–1135.

8. KawamuraT, SuzukiJ, WangYV, MenendezS, MoreraLB, et al. (2009) Linking the p53 tumour suppressor pathway to somatic cell reprogramming. Nature 460: 1140–1144.

9. LiH, ColladoM, VillasanteA, StratiK, OrtegaS, et al. (2009) The Ink4/Arf locus is a barrier for iPS cell reprogramming. Nature 460: 1136–1139.

10. MarionRM, StratiK, LiH, MurgaM, BlancoR, et al. (2009) A p53-mediated DNA damage response limits reprogramming to ensure iPS cell genomic integrity. Nature 460: 1149–1153.

11. UtikalJ, PoloJM, StadtfeldM, MaheraliN, KulalertW, et al. (2009) Immortalization eliminates a roadblock during cellular reprogramming into iPS cells. Nature 460: 1145–1148.

12. LiangG, HeJ, ZhangY (2012) Kdm2b promotes induced pluripotent stem cell generation by facilitating gene activation early in reprogramming. Nat Cell Biol 14: 457–466.

13. MansourAA, GafniO, WeinbergerL, ZviranA, AyyashM, et al. (2012) The H3K27 demethylase Utx regulates somatic and germ cell epigenetic reprogramming. Nature

14. OnderTT, KaraN, CherryA, SinhaAU, ZhuN, et al. (2012) Chromatin-modifying enzymes as modulators of reprogramming. Nature 483: 598–602.

15. WangT, ChenK, ZengX, YangJ, WuY, et al. (2011) The histone demethylases Jhdm1a/1b enhance somatic cell reprogramming in a vitamin-C-dependent manner. Cell Stem Cell 9: 575–587.

16. KocheRP, SmithZD, AdliM, GuH, KuM, et al. (2011) Reprogramming factor expression initiates widespread targeted chromatin remodeling. Cell Stem Cell 8: 96–105.

17. MaheraliN, SridharanR, XieW, UtikalJ, EminliS, et al. (2007) Directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contribution. Cell Stem Cell 1: 55–70.

18. MoreyL, HelinK (2010) Polycomb group protein-mediated repression of transcription. Trends Biochem Sci 35: 323–332.

19. MohnF, WeberM, RebhanM, RoloffTC, RichterJ, et al. (2008) Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors. Mol Cell 30: 755–766.

20. MohnF, SchubelerD (2009) Genetics and epigenetics: stability and plasticity during cellular differentiation. Trends Genet 25: 129–136.

21. BoyerLA, PlathK, ZeitlingerJ, BrambrinkT, MedeirosLA, et al. (2006) Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 441: 349–353.

22. LeeTI, JennerRG, BoyerLA, GuentherMG, LevineSS, et al. (2006) Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125: 301–313.

23. LeebM, PasiniD, NovatchkovaM, JaritzM, HelinK, et al. (2010) Polycomb complexes act redundantly to repress genomic repeats and genes. Genes Dev 24: 265–276.

24. O'CarrollD, ErhardtS, PaganiM, BartonSC, SuraniMA, et al. (2001) The polycomb-group gene Ezh2 is required for early mouse development. Mol Cell Biol 21: 4330–4336.

25. PasiniD, BrackenAP, HansenJB, CapilloM, HelinK (2007) The polycomb group protein Suz12 is required for embryonic stem cell differentiation. Mol Cell Biol 27: 3769–3779.

26. PasiniD, BrackenAP, JensenMR, Lazzerini DenchiE, HelinK (2004) Suz12 is essential for mouse development and for EZH2 histone methyltransferase activity. EMBO J 23: 4061–4071.

27. ShenX, LiuY, HsuYJ, FujiwaraY, KimJ, et al. (2008) EZH1 mediates methylation on histone H3 lysine 27 and complements EZH2 in maintaining stem cell identity and executing pluripotency. Mol Cell 32: 491–502.

28. AzuaraV, PerryP, SauerS, SpivakovM, JorgensenHF, et al. (2006) Chromatin signatures of pluripotent cell lines. Nat Cell Biol 8: 532–538.

29. BernsteinBE, MikkelsenTS, XieX, KamalM, HuebertDJ, et al. (2006) A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125: 315–326.

30. SuIH, BasavarajA, KrutchinskyAN, HobertO, UllrichA, et al. (2003) Ezh2 controls B cell development through histone H3 methylation and Igh rearrangement. Nat Immunol 4: 124–131.

31. LengnerCJ, CamargoFD, HochedlingerK, WelsteadGG, ZaidiS, et al. (2007) Oct4 expression is not required for mouse somatic stem cell self-renewal. Cell Stem Cell 1: 403–415.

32. SommerCA, StadtfeldM, MurphyGJ, HochedlingerK, KottonDN, et al. (2009) Induced pluripotent stem cell generation using a single lentiviral stem cell cassette. Stem Cells 27: 543–549.

33. YingQL, WrayJ, NicholsJ, Batlle-MoreraL, DobleB, et al. (2008) The ground state of embryonic stem cell self-renewal. Nature 453: 519–523.

34. SilvaJ, BarrandonO, NicholsJ, KawaguchiJ, TheunissenTW, et al. (2008) Promotion of reprogramming to ground state pluripotency by signal inhibition. PLoS Biol 6: e253 doi:10.1371/journal.pbio.0060253

35. BrackenAP, Kleine-KohlbrecherD, DietrichN, PasiniD, GargiuloG, et al. (2007) The Polycomb group proteins bind throughout the INK4A-ARF locus and are disassociated in senescent cells. Genes Dev 21: 525–530.

36. SerranoM, LeeH, ChinL, Cordon-CardoC, BeachD, et al. (1996) Role of the INK4a locus in tumor suppression and cell mortality. Cell 85: 27–37.

37. MargueronR, LiG, SarmaK, BlaisA, ZavadilJ, et al. (2008) Ezh1 and Ezh2 maintain repressive chromatin through different mechanisms. Mol Cell 32: 503–518.

38. HansenM, GerdsTA, NielsenOH, SeidelinJB, TroelsenJT, et al. (2012) pcaGoPromoter–an R package for biological and regulatory interpretation of principal components in genome-wide gene expression data. PLoS ONE 7: e32394 doi:10.1371/journal.pone.0032394

39. EzhkovaE, LienWH, StokesN, PasolliHA, SilvaJM, et al. (2011) EZH1 and EZH2 cogovern histone H3K27 trimethylation and are essential for hair follicle homeostasis and wound repair. Genes Dev 25: 485–498.

40. SimonJA, KingstonRE (2009) Mechanisms of polycomb gene silencing: knowns and unknowns. Nat Rev Mol Cell Biol 10: 697–708.

41. MargueronR, ReinbergD (2011) The Polycomb complex PRC2 and its mark in life. Nature 469: 343–349.

42. EzhkovaE, PasolliHA, ParkerJS, StokesN, SuIH, et al. (2009) Ezh2 orchestrates gene expression for the stepwise differentiation of tissue-specific stem cells. Cell 136: 1122–1135.

43. HirabayashiY, SuzkiN, TsuboiM, EndoTA, ToyodaT, et al. (2009) Polycomb limits the neurogenic competence of neural precursor cells to promote astrogenic fate transition. Neuron 63: 600–613.

44. TestaG (2011) The time of timing: How Polycomb proteins regulate neurogenesis. Bioessays 33: 519–528.

45. PereiraCF, PiccoloFM, TsubouchiT, SauerS, RyanNK, et al. (2010) ESCs require PRC2 to direct the successful reprogramming of differentiated cells toward pluripotency. Cell Stem Cell 6: 547–556.

46. MunstB, PatschC, EdenhoferF (2009) Engineering cell-permeable protein. J Vis Exp

47. IrizarryRA, HobbsB, CollinF, Beazer-BarclayYD, AntonellisKJ, et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249–264.

48. GentlemanRC, CareyVJ, BatesDM, BolstadB, DettlingM, et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80.

49. ReinerA, YekutieliD, BenjaminiY (2003) Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics 19: 368–375.

50. MaereS, HeymansK, KuiperM (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 21: 3448–3449.

51. SmootME, OnoK, RuscheinskiJ, WangPL, IdekerT (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27: 431–432.

52. LangmeadB, TrapnellC, PopM, SalzbergSL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.

53. ZhangY, LiuT, MeyerCA, EeckhouteJ, JohnsonDS, et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol 9: R137.

54. SongQ, SmithAD (2011) Identifying dispersed epigenomic domains from ChIP-Seq data. Bioinformatics 27: 870–871.

55. MicsinaiM, ParisiF, StrinoF, AspP, DynlachtBD, et al. (2012) Picking ChIP-seq peak detectors for analyzing chromatin modification experiments. Nucleic Acids Res 40: e70.

56. KinsellaRJ, KahariA, HaiderS, ZamoraJ, ProctorG, et al. (2011) Ensembl BioMarts: a hub for data retrieval across taxonomic space. Database (Oxford) 2011: bar030.

57. YeT, KrebsAR, ChoukrallahMA, KeimeC, PlewniakF, et al. (2011) seqMINER: an integrated ChIP-seq data interpretation platform. Nucleic Acids Res 39: e35.