1. AzuaraV, PerryP, SauerS, SpivakovM, JorgensenHF, et al. (2006) Chromatin signatures of pluripotent cell lines. Nat Cell Biol 8: 532–538.
2. BernsteinBE, MikkelsenTS, XieX, KamalM, HuebertDJ, et al. (2006) A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125: 315–326.
3. KuM, KocheRP, RheinbayE, MendenhallEM, EndohM, et al. (2008) Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet 4: e1000242.
4. MikkelsenTS, KuM, JaffeDB, IssacB, LiebermanE, et al. (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448: 553–560.
5. Rugg-GunnPJ, CoxBJ, RalstonA, RossantJ (2010) Distinct histone modifications in stem cell lines and tissue lineages from the early mouse embryo. Proc Natl Acad Sci U S A 107: 10783–10790.
6. SachsM, OnoderaC, BlaschkeK, EbataKT, SongJS, et al. (2013) Bivalent Chromatin Marks Developmental Regulatory Genes in the Mouse Embryonic Germline In Vivo. Cell Rep 3: 1777–84 doi: 10.1016/j.celrep.2013.04.032
7. HammoudSS, NixDA, ZhangH, PurwarJ, CarrellDT, et al. (2009) Distinctive chromatin in human sperm packages genes for embryo development. Nature 460: 473–478.
8. LindemanLC, AndersenIS, ReinerAH, LiN, AanesH, et al. (2011) Prepatterning of developmental gene expression by modified histones before zygotic genome activation. Dev Cell 21: 993–1004.
9. DahlJA, ReinerAH, KlunglandA, WakayamaT, CollasP (2010) Histone H3 lysine 27 methylation asymmetry on developmentally-regulated promoters distinguish the first two lineages in mouse preimplantation embryos. PLoS One 5: e9150.
10. AlderO, LavialF, HelnessA, BrookesE, PinhoS, et al. (2010) Ring1B and Suv39h1 delineate distinct chromatin states at bivalent genes during early mouse lineage commitment. Development 137: 2483–2492.
11. CuiK, ZangC, RohTY, SchonesDE, ChildsRW, et al. (2009) Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation. Cell Stem Cell 4: 80–93.
12. van ArensbergenJ, Garcia-HurtadoJ, MoranI, MaestroMA, XuX, et al. (2010) Derepression of Polycomb targets during pancreatic organogenesis allows insulin-producing beta-cells to adopt a neural gene activity program. Genome Res 20: 722–732.
13. RohTY, CuddapahS, CuiK, ZhaoK (2006) The genomic landscape of histone modifications in human T cells. Proc Natl Acad Sci U S A 103: 15782–15787.
14. ZhaoXD, HanX, ChewJL, LiuJ, ChiuKP, et al. (2007) Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells. Cell Stem Cell 1: 286–298.
15. PanG, TianS, NieJ, YangC, RuottiV, et al. (2007) Whole-genome analysis of histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells. Cell Stem Cell 1: 299–312.
16. WangAH, ZareH, MousaviK, WangC, MoravecCE, et al. (2013) The histone chaperone Spt6 coordinates histone H3K27 demethylation and myogenesis. EMBO J 32: 1075–1086.
17. KartikasariAE, ZhouJX, KanjiMS, ChanDN, SinhaA, et al. (2013) The histone demethylase Jmjd3 sequentially associates with the transcription factors Tbx3 and Eomes to drive endoderm differentiation. EMBO J 32: 1393–1408.
18. RamadossS, ChenX, WangCY (2012) Histone demethylase KDM6B promotes epithelial-mesenchymal transition. J Biol Chem 287: 44508–44517.
19. JiangW, WangJ, ZhangY (2012) Histone H3K27me3 demethylases KDM6A and KDM6B modulate definitive endoderm differentiation from human ESCs by regulating WNT signaling pathway. Cell Res 23: 122–130.
20. WangJK, TsaiMC, PoulinG, AdlerAS, ChenS, et al. (2010) The histone demethylase UTX enables RB-dependent cell fate control. Genes Dev 24: 327–332.
21. SeenundunS, RampalliS, LiuQC, AzizA, PaliiC, et al. (2010) UTX mediates demethylation of H3K27me3 at muscle-specific genes during myogenesis. EMBO J 29: 1401–1411.
22. BurgoldT, SpreaficoF, De SantaF, TotaroMG, ProsperiniE, et al. (2008) The histone H3 lysine 27-specific demethylase Jmjd3 is required for neural commitment. PLoS One 3: e3034.
23. SatohT, TakeuchiO, VandenbonA, YasudaK, TanakaY, et al. (2010) The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection. Nat Immunol 11: 936–944.
24. SenGL, WebsterDE, BarraganDI, ChangHY, KhavariPA (2008) Control of differentiation in a self-renewing mammalian tissue by the histone demethylase JMJD3. Genes Dev 22: 1865–1870.
25. BarradasM, AndertonE, AcostaJC, LiS, BanitoA, et al. (2009) Histone demethylase JMJD3 contributes to epigenetic control of INK4a/ARF by oncogenic RAS. Genes Dev 23: 1177–1182.
26. AggerK, CloosPA, RudkjaerL, WilliamsK, AndersenG, et al. (2009) The H3K27me3 demethylase JMJD3 contributes to the activation of the INK4A-ARF locus in response to oncogene- and stress-induced senescence. Genes Dev 23: 1171–1176.
27. LanF, BaylissPE, RinnJL, WhetstineJR, WangJK, et al. (2007) A histone H3 lysine 27 demethylase regulates animal posterior development. Nature 449: 689–694.
28. De SantaF, TotaroMG, ProsperiniE, NotarbartoloS, TestaG, et al. (2007) The histone H3 lysine-27 demethylase Jmjd3 links inflammation to inhibition of polycomb-mediated gene silencing. Cell 130: 1083–1094.
29. AggerK, CloosPA, ChristensenJ, PasiniD, RoseS, et al. (2007) UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development. Nature 449: 731–734.
30. LeeMG, VillaR, TrojerP, NormanJ, YanKP, et al. (2007) Demethylation of H3K27 regulates polycomb recruitment and H2A ubiquitination. Science 318: 447–450.
31. ShpargelKB, SengokuT, YokoyamaS, MagnusonT (2012) UTX and UTY demonstrate histone demethylase-independent function in mouse embryonic development. PLoS Genet 8: e1002964.
32. WangC, LeeJE, ChoYW, XiaoY, JinQ, et al. (2012) UTX regulates mesoderm differentiation of embryonic stem cells independent of H3K27 demethylase activity. Proc Natl Acad Sci U S A 109: 15324–15329.
33. HongS, ChoYW, YuLR, YuH, VeenstraTD, et al. (2007) Identification of JmjC domain-containing UTX and JMJD3 as histone H3 lysine 27 demethylases. Proc Natl Acad Sci U S A 104: 18439–18444.
34. WalportLJ, HopkinsonRJ, VollmarM, MaddenSK, GileadiC, et al. (2014) Human UTY(KDM6C) is a Male-Specific N-Methyl Lysyl-Demethylase. J Biol Chem 289: 18302–18313.
35. BurgoldT, VoituronN, CaganovaM, TripathiPP, MenuetC, et al. (2012) The H3K27 demethylase JMJD3 is required for maintenance of the embryonic respiratory neuronal network, neonatal breathing, and survival. Cell Rep 2: 1244–1258.
36. ChamberlainSJ, YeeD, MagnusonT (2008) Polycomb repressive complex 2 is dispensable for maintenance of embryonic stem cell pluripotency. Stem Cells 26: 1496–1505.
37. FaustC, SchumacherA, HoldenerB, MagnusonT (1995) The eed mutation disrupts anterior mesoderm production in mice. Development 121: 273–285.
38. PasiniD, BrackenAP, JensenMR, Lazzerini DenchiE, HelinK (2004) Suz12 is essential for mouse development and for EZH2 histone methyltransferase activity. EMBO J 23: 4061–4071.
39. 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.
40. CopurO, MullerJ (2013) The histone H3-K27 demethylase Utx regulates HOX gene expression in Drosophila in a temporally restricted manner. Development 140: 3478–3485.
41. HayashiS, McMahonAP (2002) Efficient recombination in diverse tissues by a tamoxifen-inducible form of Cre: a tool for temporally regulated gene activation/inactivation in the mouse. Dev Biol 244: 305–318.
42. WalkerE, ChangWY, HunkapillerJ, CagneyG, GarchaK, et al. (2010) Polycomb-like 2 associates with PRC2 and regulates transcriptional networks during mouse embryonic stem cell self-renewal and differentiation. Cell Stem Cell 6: 153–166.
43. ZhangH, BradleyA (1996) Mice deficient for BMP2 are nonviable and have defects in amnion/chorion and cardiac development. Development 122: 2977–2986.
44. MeyersEN, LewandoskiM, MartinGR (1998) An Fgf8 mutant allelic series generated by Cre- and Flp-mediated recombination. Nat Genet 18: 136–141.
45. MolkentinJD, LinQ, DuncanSA, OlsonEN (1997) Requirement of the transcription factor GATA4 for heart tube formation and ventral morphogenesis. Genes Dev 11: 1061–1072.
46. MorriseyEE, TangZ, SigristK, LuMM, JiangF, et al. (1998) GATA6 regulates HNF4 and is required for differentiation of visceral endoderm in the mouse embryo. Genes Dev 12: 3579–3590.
47. ArnoldSJ, HofmannUK, BikoffEK, RobertsonEJ (2008) Pivotal roles for eomesodermin during axis formation, epithelium-to-mesenchyme transition and endoderm specification in the mouse. Development 135: 501–511.
48. RussAP, WattlerS, ColledgeWH, AparicioSA, CarltonMB, et al. (2000) Eomesodermin is required for mouse trophoblast development and mesoderm formation. Nature 404: 95–99.
49. HerrmannBG (1991) Expression pattern of the Brachyury gene in whole-mount TWis/TWis mutant embryos. Development 113: 913–917.
50. WinnierG, BlessingM, LaboskyPA, HoganBL (1995) Bone morphogenetic protein-4 is required for mesoderm formation and patterning in the mouse. Genes Dev 9: 2105–2116.
51. LiuP, WakamiyaM, SheaMJ, AlbrechtU, BehringerRR, et al. (1999) Requirement for Wnt3 in vertebrate axis formation. Nat Genet 22: 361–365.
52. CarverEA, JiangR, LanY, OramKF, GridleyT (2001) The mouse snail gene encodes a key regulator of the epithelial-mesenchymal transition. Mol Cell Biol 21: 8184–8188.
53. XieW, SchultzMD, ListerR, HouZ, RajagopalN, et al. (2013) Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell 153: 1134–1148.
54. GiffordCA, ZillerMJ, GuH, TrapnellC, DonagheyJ, et al. (2013) Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells. Cell 153: 1149–1163.
55. MansourAA, GafniO, WeinbergerL, ZviranA, AyyashM, et al. (2012) The H3K27 demethylase Utx regulates somatic and germ cell epigenetic reprogramming. Nature 488: 409–413.
56. WelsteadGG, CreyghtonMP, BilodeauS, ChengAW, MarkoulakiS, et al. (2012) X-linked H3K27me3 demethylase Utx is required for embryonic development in a sex-specific manner. Proc Natl Acad Sci U S A 109: 13004–13009.
57. Morales TorresC, LaugesenA, HelinK (2013) Utx is required for proper induction of ectoderm and mesoderm during differentiation of embryonic stem cells. PLoS One 8: e60020.
58. ShahhoseiniM, TaghizadehZ, HatamiM, BaharvandH (2013) Retinoic acid dependent histone 3 demethylation of the clustered HOX genes during neural differentiation of human embryonic stem cells. Biochem Cell Biol 91: 116–122.
59. LeeS, LeeJW, LeeSK (2012) UTX, a Histone H3-Lysine 27 Demethylase, Acts as a Critical Switch to Activate the Cardiac Developmental Program. Dev Cell
60. HuangC, XiangY, WangY, LiX, XuL, et al. (2010) Dual-specificity histone demethylase KIAA1718 (KDM7A) regulates neural differentiation through FGF4. Cell Res 20: 154–165.
61. LoenarzC, GeW, ColemanML, RoseNR, CooperCD, et al. (2010) PHF8, a gene associated with cleft lip/palate and mental retardation, encodes for an Nepsilon-dimethyl lysine demethylase. Hum Mol Genet 19: 217–222.
62. YuL, WangY, HuangS, WangJ, DengZ, et al. (2010) Structural insights into a novel histone demethylase PHF8. Cell Res 20: 166–173.
63. SengokuT, YokoyamaS (2011) Structural basis for histone H3 Lys 27 demethylation by UTX/KDM6A. Genes Dev 25: 2266–2277.
64. ChenZ, ZangJ, KapplerJ, HongX, CrawfordF, et al. (2007) Structural basis of the recognition of a methylated histone tail by JMJD2A. Proc Natl Acad Sci U S A 104: 10818–10823.
65. DealRB, HenikoffJG, HenikoffS (2010) Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones. Science 328: 1161–1164.
66. HansenKH, BrackenAP, PasiniD, DietrichN, GehaniSS, et al. (2008) A model for transmission of the H3K27me3 epigenetic mark. Nat Cell Biol 10: 1291–1300.
67. PetrukS, SedkovY, JohnstonDM, HodgsonJW, BlackKL, et al. (2012) TrxG and PcG proteins but not methylated histones remain associated with DNA through replication. Cell 150: 922–933.
68. FrancisNJ, FollmerNE, SimonMD, AghiaG, ButlerJD (2009) Polycomb proteins remain bound to chromatin and DNA during DNA replication in vitro. Cell 137: 110–122.
69. InoueA, ZhangY (2011) Replication-dependent loss of 5-hydroxymethylcytosine in mouse preimplantation embryos. Science 334: 194.
70. OhnoR, NakayamaM, NaruseC, OkashitaN, TakanoO, et al. (2013) A replication-dependent passive mechanism modulates DNA demethylation in mouse primordial germ cells. Development 140: 2892–903 doi: 10.1242/dev.093229
71. MillerSA, MohnSE, WeinmannAS (2010) Jmjd3 and UTX play a demethylase-independent role in chromatin remodeling to regulate T-box family member-dependent gene expression. Mol Cell 40: 594–605.
72. VandammeJ, LettierG, SidoliS, Di SchiaviE, Norregaard JensenO, et al. (2012) The C. elegans H3K27 demethylase UTX-1 is essential for normal development, independent of its enzymatic activity. PLoS Genet 8: e1002647.
73. GallardoT, ShirleyL, JohnGB, CastrillonDH (2007) Generation of a germ cell-specific mouse transgenic Cre line, Vasa-Cre. Genesis 45: 413–417.
74. RahlPB, LinCY, SeilaAC, FlynnRA, McCuineS, et al. (2010) c-Myc regulates transcriptional pause release. Cell 141: 432–445.
75. CalabreseJM, SunW, SongL, MugfordJW, WilliamsL, et al. (2012) Site-specific silencing of regulatory elements as a mechanism of X inactivation. Cell 151: 951–963.