Regulation beyond genome sequences: DNA and histone
methylation in embryonic stem cells

doi:10.1007/s11515-010-0006-9

Front. Biol.

2010, Vol. 5

Issue (1) : 41-47 https://doi.org/10.1007/s11515-010-0006-9

Research articles

Regulation beyond genome sequences: DNA and histone methylation in embryonic stem cells

Wei YANG¹,Qi ZHOU²,Xiu-Jie WANG³,

1.State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China；Graduate University of the Chinese Academy of Sciences, Beijing 100101, China; 2.State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; 3.State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;

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Abstract Embryonic stem (ES) cells distinct themselves from other cell type populations by their pluripotent ability. The unique features of ES cells are controlled by both genetic and epigenetic factors. Studies have shown that the methylation status of DNA and histones in ES cells is quite different from that of differentiated cells and somatic stem cells. Herein, we summarized recent advances in DNA and histone methylation studies of mammalian ES cells. The methylation status of several key pluripotent regulatory genes is also discussed.

Keywords Embryonic stem (ES) cells epigenetic DNA methylation histone methylation

Issue Date: 01 February 2010

Cite this article:

Wei YANG,Qi ZHOU,Xiu-Jie WANG. Regulation beyond genome sequences: DNA and histone methylation in embryonic stem cells[J]. Front. Biol., 2010, 5(1): 41-47.

URL:

https://academic.hep.com.cn/fib/EN/10.1007/s11515-010-0006-9
https://academic.hep.com.cn/fib/EN/Y2010/V5/I1/41

	Avilion A A, Nicolis S K, Pevny L H, Perez L, Vivian N, Lovell-Badge R (2003). Multipotent cell lineages in early mouse developmentdepend on SOX2 function. Genes Dev, 17(1): 126―140 doi: 10.1101/gad.224503
	Barski A, Cuddapah S, Cui K, Roh T Y, Schones D E, Wang Z, Wei G, Chepelev I, Zhao K (2007). High-resolution profiling of histone methylations inthe human genome. Cell, 129(4): 823―837 doi: 10.1016/j.cell.2007.05.009
	Benevolenskaya E V (2007). Histone H3K4 demethylases are essential in developmentand differentiation. Biochem Cell Biol, 85(4): 435―443 doi: 10.1139/O07-057
	Bernstein B E, Mikkelsen T S, Xie X, Kamal M, Huebert D J, Cuff J, Fry B, Meissner A, Wernig M, Plath K (2006). A bivalentchromatin structure marks key developmental genes in embryonic stemcells. Cell, 125(2): 315―326 doi: 10.1016/j.cell.2006.02.041
	Bibikova M, Chudin E, Wu B, Zhou L, Garcia E W, Liu Y, Shin S, Plaia T W, Auerbach J M, Arking D (2006). Humanembryonic stem cells have a unique epigenetic signature. Genome Res, 16(9): 1075―1083 doi: 10.1101/gr.5319906
	Bibikova M, Laurent L C, Ren B, Loring J F, Fan J B (2008). Unraveling epigeneticregulation in embryonic stem cells. CellStem Cell, 2(2): 123―134 doi: 10.1016/j.stem.2008.01.005
	Bird A (2002). DNA methylation patterns and epigenetic memory. Genes Dev, 16(1): 6―21 doi: 10.1101/gad.947102
	Brambrink T, Foreman R, Welstead G G, Lengner C J, Wernig M, Suh H, Jaenisch R (2008). Sequential expression of pluripotency markers duringdirect reprogramming of mouse somatic cells. Cell Stem Cell, 2(2): 151―159 doi: 10.1016/j.stem.2008.01.004
	Callinan P A, Feinberg A P (2006). The emergingscience of epigenomics. Hum Mol Genet 15Spec No, 1: R95―R101
	Chambers I, Colby D, Robertson M, Nichols J, Lee S, Tweedie S, Smith A (2003). Functional expression cloning of Nanog, a pluripotency sustainingfactor in embryonic stem cells. Cell, 113(5): 643―655 doi: 10.1016/S0092-8674(03)00392-1
	Chin M H, Mason M J, Xie W, Volinia S, Singer M, Peterson C, Ambartsumyan G, Aimiuwu O, Richter L, Zhang J (2009). Induced pluripotent stem cells and embryonic stem cells are distinguishedby gene expression signatures. Cell StemCell, 5(1): 111―123 doi: 10.1016/j.stem.2009.06.008
	Dodge J E, Ramsahoye B H, Wo Z G, Okano M, Li E (2002). De novo methylationof MMLV provirus in embryonic stem cells: CpG versus non-CpG methylation. Gene, 289(1－2): 41―48 doi: 10.1016/S0378-1119(02)00469-9
	Fouse S D, Shen Y, Pellegrini M, Cole S, Meissner A, Van Neste L, Jaenisch R, Fan G (2008). Promoter CpG methylation contributesto ES cell gene regulation in parallel with Oct4/Nanog, PcG complex,and histone H3 K4/K27 trimethylation. CellStem Cell, 2(2): 160―169 doi: 10.1016/j.stem.2007.12.011
	Fraga M F, Esteller M (2002). DNA methylation:a profile of methods and applications. Biotechniques, 33(3): 632, 634, 636―649
	Goldberg A D, Allis C D, Bernstein E (2007). Epigenetics: a landscape takes shape. Cell, 128(4): 635―638 doi: 10.1016/j.cell.2007.02.006
	Haines T R, Rodenhiser D I, Ainsworth P J (2001). Allele-specific non-CpG methylationof the Nf1 gene during early mouse development. Dev Biol, 240(2): 585―598 doi: 10.1006/dbio.2001.0504
	Hochedlinger K, Plath K (2009). Epigeneticreprogramming and induced pluripotency. Development, 136(4): 509―523 doi: 10.1242/dev.020867
	Ikegami K, Iwatani M, Suzuki M, Tachibana M, Shinkai Y, Tanaka S, Greally J M, Yagi S, Hattori N, Shiota K (2007). Genome-wide and locus-specific DNA hypomethylation in G9a deficientmouse embryonic stem cells. Genes Cells, 12(1): 1―11 doi: 10.1111/j.1365-2443.2006.01029.x
	Jackson J P, Lindroth A M, Cao X, Jacobsen S E (2002). Control of CpNpG DNA methylation by the KRYPTONITE histoneH3 methyltransferase. Nature, 416(6880): 556―560 doi: 10.1038/nature731
	Jeffares D C, Poole A M, Penny D (1998). Relics from the RNA world. J Mol Evol, 46(1): 18―36 doi: 10.1007/PL00006280
	Jenuwein T, Allis C D (2001). Translatingthe histone code. Science, 293(5532): 1074―1080 doi: 10.1126/science.1063127
	Jones P A, Baylin S B (2002). The fundamentalrole of epigenetic events in cancer. NatRev Genet, 3(6): 415―428
	Keller G (2005). Embryonic stem cell differentiation: emergence of anew era in biology and medicine. GenesDev, 19(10): 1129―1155 doi: 10.1101/gad.1303605
	Khulan B, Thompson R F, Ye K, Fazzari M J, Suzuki M, Stasiek E, Figueroa M E, Glass J L, Chen Q, Montagna C (2006). Comparative isoschizomer profiling of cytosine methylation:the HELP assay. Genome Res, 16(8): 1046―1055 doi: 10.1101/gr.5273806
	Koch C M, Andrews R M, Flicek P, Dillon S C, Kara z U, Clelland G K, Wilcox S, Beare D M, Fowler J C, Couttet P (2007). The landscapeof histone modifications across 1% of the human genome in five humancell lines. Genome Res, 17(6): 691―707 doi: 10.1101/gr.5704207
	Lachner M, Jenuwein T (2002). The manyfaces of histone lysine methylation. CurrOpin Cell Biol, 14(3): 286―298 doi: 10.1016/S0955-0674(02)00335-6
	Latham T, Gilbert N, Ramsahoye B (2008). DNA methylation in mouse embryonicstem cells and development. Cell TissueRes, 331(1): 31―55 doi: 10.1007/s00441-007-0537-9
	Lehnertz B, Ueda Y, Derijck Aaha, Braunschweig U, Perez-Burgos L, Kubicek S, Chen T, Li E, Jenuwein T, Peters A (2003). Suv39h-mediatedhistone H3 lysine 9 methylation directs DNA methylation to major satelliterepeats at pericentric heterochromatin. Curr Biol, 13(14): 1192―1200 doi: 10.1016/S0960-9822(03)00432-9
	Li E (2002). Chromatin modification and epigenetic reprogrammingin mammalian development. Nat Rev Genet, 3(9): 662―673 doi: 10.1038/nrg887
	Lister R, Pelizzola M, Dowen R H, Hawkins R D, Hon G, Tonti-Filippini J, Nery J R, Lee L, Ye Z, Ngo Q M (2009). Human DNA methylomes at base resolution show widespread epigenomicdifferences. Nature, 462: 315―322 doi: 10.1038/nature08514
	Luger K, Mader A W, Richmond R K, Sargent D F, Richmond T J (1997). Crystalstructure of the nucleosome core particle at 2.8 A resolution. Nature, 389(6648): 251―260 doi: 10.1038/38444
	Meissner A, Mikkelsen T S, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein B E, Nusbaum C, Jaffe D B (2008). Genome-scale DNA methylation maps of pluripotent and differentiatedcells. Nature, 454(7205): 766―770
	Meshorer E, Misteli T (2006). Chromatinin pluripotent embryonic stem cells and differentiation. Nat Rev Mol Cell Biol, 7(7): 540―546 doi: 10.1038/nrm1938
	Mikkelsen T S, Ku M, Jaffe D B, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim T K, Koche R P (2007). Genome-wide maps of chromatin state in pluripotent and lineage-committedcells. Nature, 448(7153): 553―560 doi: 10.1038/nature06008
	Narlikar G J, Fan H Y, Kingston R E (2002). Cooperation between complexes thatregulate chromatin structure and transcription. Cell, 108(4): 475―487 doi: 10.1016/S0092-8674(02)00654-2
	Ng S S, Yue W W, Oppermann U, Klose R J (2009). Dynamic protein methylation in chromatin biology. Cell Mol Life Sci, 66(3): 407―422 doi: 10.1007/s00018-008-8303-z
	Nichols J, Zevnik B, Anastassiadis K, Niwa H, Klewe-Nebenius D, Chambers I (1998). Formation of pluripotent stem cellsin the mammalian embryo depends on the POU transcription factor Oct4. Cell, 95(3): 379―391 doi: 10.1016/S0092-8674(00)81769-9
	Niwa H, Miyazaki J, Smith A G (2000). Quantitative expression of Oct-3/4defines differentiation, dedifferentiation or self-renewal of ES cells. Nat Genet, 24(4): 372―376 doi: 10.1038/74199
	Ooi S K, Qiu C, Bernstein E, Li K, Jia D, Yang Z, Erdjument-Bromage H, Tempst P, Lin S P, Allis C D(2007). DNMT3Lconnects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature448(7154): 714―717 doi: 10.1038/nature05987
	Pan G, Tian S, Nie J, Yang C, Ruotti V, Wei H, Jonsdottir G A, Stewart R, Thomson J A (2007). Whole-genome analysis of histone H3 lysine 4 and lysine27 methylation in human embryonic stem cells. Cell Stem Cell, 1(3): 299―312 doi: 10.1016/j.stem.2007.08.003
	Roth S Y, Denu J M, Allis C D (2001). Histone acetyltransferases. Annu Rev Biochem, 70: 81―120 doi: 10.1146/annurev.biochem.70.1.81
	Shi Y, Do J T, Desponts C, Hahm H S, Schöler H R, Ding S (2008). A combined chemical and genetic approachfor the generation of induced pluripotent stem cells. Cell Stem Cell, 2(6): 525―528 doi: 10.1016/j.stem.2008.05.011
	Shiota K, Kogo Y, Ohgane J, Imamura T, Urano A, Nishino K, Tanaka S, Hattori N (2002). Epigenetic marks byDNA methylation specific to stem, germ and somatic cells in mice. Genes Cells, 7(9): 961―969 doi: 10.1046/j.1365-2443.2002.00574.x
	Silva J, Smith A (2008). Capturingpluripotency. Cell, 132(4): 532―536 doi: 10.1016/j.cell.2008.02.006
	Smith A G (2001). Embryo-derived stem cells: of mice and men. Annu Rev Cell Dev Biol, 17: 435―462 doi: 10.1146/annurev.cellbio.17.1.435
	Steger D J, Lefterova M I, Ying L, Stonestrom A J, Schupp M, Zhuo D, Vakoc A L, Kim J E, Chen J, Lazar M A (2008). DOT1L/KMT4recruitment and H3K79 methylation are ubiquitously coupled with genetranscription in mammalian cells. Mol CellBiol, 28(8): 2825―2839 doi: 10.1128/MCB.02076-07
	Strahl B D, Allis C D (2000). The languageof covalent histone modifications. Nature, 403(6765): 41―45 doi: 10.1038/47412
	Takahashi K, Tanabe K, Ohnuki M, Narita M, Ichisaka T, Tomoda K, Yamanaka S (2007). Inductionof pluripotent stem cells from adult human fibroblasts by definedfactors. Cell, 131(5): 861―872 doi: 10.1016/j.cell.2007.11.019
	Takahashi K, Yamanaka S (2006). Inductionof pluripotent stem cells from mouse embryonic and adult fibroblastcultures by defined factors. Cell, 126(4): 663―676 doi: 10.1016/j.cell.2006.07.024
	Tamaru H, Selker E U (2001). A histoneH3 methyltransferase controls DNA methylation in Neurospora crassa. Nature, 414(6861): 277―283 doi: 10.1038/35104508
	Torres-Padilla M E, Parfitt D E, Kouzarides T, Zernicka-Goetz M (2007). Histone arginine methylation regulates pluripotencyin the early mouse embryo. Nature, 445(7124): 214―218 doi: 10.1038/nature05458
	Tucker K L (2001). Methylated cytosine and the brain: a new base for neuroscience. Neuron, 30(3): 649―652 doi: 10.1016/S0896-6273(01)00325-7
	Weber M, Davies J J, Wittig D, Oakeley E J, Haase M, Lam W L, Schubeler D (2005). Chromosome-wide and promoter-specific analyses identifysites of differential DNA methylation in normal and transformed humancells. Nat Genet, 37(8): 853―862 doi: 10.1038/ng1598
	Wu C, Morris J R (2001). Genes,genetics, and epigenetics: a correspondence. Science, 293(5532): 1103―1105 doi: 10.1126/science.293.5532.1103
	Yeo S, Jeong S, Kim J, Han J S, Han Y M, Kang Y K (2007). Characterization of DNA methylation change in stem cellmarker genes during differentiation of human embryonic stem cells. Biochem Biophys Res Commun, 359(3): 536―542 doi: 10.1016/j.bbrc.2007.05.120
	Zhao X, Ruan Y, Wei C L (2008). Tackling the epigenome in the pluripotentstem cells. J Genet Genomics, 35(7): 403―412 doi: 10.1016/S1673-8527(08)60058-2
	Zhao X D, Han X, Chew J L, Liu J, Chiu K P, Choo A, Orlov Y L, Sung W K, Shahab A, Kuznetsov V A (2007). Whole-genomemapping of histone H3 Lys4 and 27 trimethylations reveals distinctgenomic compartments in human embryonic stem cells. Cell Stem Cell, 1(3): 286―298 doi: 10.1016/j.stem.2007.08.004

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