Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

Nature
Tarjei S MikkelsenBradley E Bernstein

Abstract

We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.

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Mar 26, 2009·Annual Review of Biochemistry·Oliver J Rando, Howard Y Chang
Jul 7, 2009·Annual Review of Cell and Developmental Biology·Shenghui HeSean J Morrison
Sep 5, 2008·Annual Review of Genomics and Human Genetics·Ky Sha
Jun 26, 2008·Annual Review of Genomics and Human Genetics·Elaine R Mardis
May 8, 2010·Journal of Applied Physiology·Susana Gonzalo
Jun 16, 2012·Comparative and Functional Genomics·Maria J Barrero
Jun 16, 2012·Comparative and Functional Genomics·Raffaella Fittipaldi, Giuseppina Caretti
Oct 3, 2008·Cancer Research·Joo Mi YiStephen B Baylin
Jun 17, 2011·Cancer Research·Ram-Shankar ManiArul M Chinnaiyan
May 17, 2012·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Elizabeth R Lawlor, Carol J Thiele
Jul 8, 2010·Cytogenetic and Genome Research·A M Khalil, D J Driscoll
Aug 7, 2010·Circulation Research·Alika K MaunakeaKeji Zhao
Feb 26, 2013·The Journal of Clinical Investigation·Nuria C BramswigKlaus H Kaestner
Nov 10, 2013·The Journal of Clinical Investigation·Klaus W WagnerMin Gyu Lee
Nov 10, 2013·The Journal of Clinical Investigation·Marieta CaganovaStefano Casola
Dec 24, 2010·Journal of Dental Research·Dashzeveg Bayarsaihan
Nov 14, 2012·Therapeutic Advances in Endocrinology and Metabolism·Andreas Soejitno, Pande Kadek Aditya Prayudi
May 20, 2009·BMC Bioinformatics·Alexandre GattikerMichael Primig
Sep 24, 2009·BMC Bioinformatics·Christiana SpyrouSimon Tavaré
Mar 11, 2010·BMC Bioinformatics·Florian BattkeKay Nieselt
Jul 6, 2010·BMC Bioinformatics·Zhaohui S QinArul M Chinnaiyan
Aug 10, 2010·BMC Bioinformatics·Mali Salmon-DivonPaul Bertone
Sep 11, 2010·BMC Bioinformatics·David A NixSamir J Courdy
Nov 16, 2010·BMC Bioinformatics·Jessica L Larson, Guo-Cheng Yuan
Mar 5, 2010·BMC Bioinformatics·Ravi GuptaRamana V Davuluri
May 11, 2011·BMC Bioinformatics·Xin FengLincoln Stein
Jul 9, 2011·BMC Bioinformatics·Eugenia G Giannopoulou, Olivier Elemento
Feb 2, 2011·BMC Bioinformatics·Peter HumburgGlenn Stone
Oct 25, 2011·BMC Bioinformatics·Luca PinelloGuo-Cheng Yuan
Jan 18, 2013·BMC Bioinformatics·Yuan JiShoudan Liang
Mar 1, 2008·BMC Bioinformatics·Andrew D SmithMichael Q Zhang
Oct 15, 2008·BMC Bioinformatics·Jacques RougemontFelix Naef
Dec 20, 2008·BMC Bioinformatics·Kyoung-Jae WonWei Wang
Aug 2, 2011·BMC Developmental Biology·Istvan GyurjánDenis Duboule
Apr 2, 2009·BMC Genomics·Jeffrey A RosenfeldMichael Q Zhang
Nov 26, 2009·BMC Genomics·Katharina Sarah HeyseHans-Joachim Lipps
Aug 4, 2012·BMC Genomics·Zhong Wang, Huntington F Willard
Jan 11, 2013·BMC Genomics·Yupeng HeChaochun Wei
Mar 21, 2013·BMC Genomics·Brian J AbrahamKeji Zhao
Feb 14, 2013·BMC Genomics·Milos PjanicNicolas Mermod
Dec 22, 2011·BMC Molecular Biology·Samuel RiveroJosé J García-Ramírez
Apr 30, 2008·BMC Neuroscience·Yan JiangSchahram Akbarian
Jun 10, 2010·BMC Biology·Edison T LiuMikael Huss
Jul 20, 2012·BMC Systems Biology·Xi Wang, Xuegong Zhang
Dec 3, 2011·BMC Medical Genomics·Jung-Hoon ParkYoung-Joon Kim
Aug 17, 2010·BioData Mining·Stefan EnrothJan Komorowski
Dec 18, 2009·BMC Research Notes·Nicolas Buisine, Laurent Sachs
Jan 17, 2012·BMC Research Notes·Petr KlusBrian Yh Lam
Feb 26, 2010·Epigenetics & Chromatin·Kirsten R McEwen, Anne C Ferguson-Smith
Jul 22, 2011·Epigenetics & Chromatin·Irina A MaksakovaMatthew C Lorincz
Aug 5, 2011·Epigenetics & Chromatin·Brandon J ThomasAnton Krumm
Jun 8, 2011·Epigenetics & Chromatin·Marco De GobbiDouglas R Higgs
Aug 9, 2012·Epigenetics & Chromatin·Peggy PrickaertsJ Willem Voncken
Oct 2, 2012·Mobile DNA·Andrew B Conley, I King Jordan
Nov 7, 2012·Cell & Bioscience·Catherine Lee, Nobuaki Kikyo
Feb 7, 2014·Cell & Bioscience·Jing Huang
Dec 18, 2008·Genome Biology·France DenoeudFrançois Artiguenave
Sep 19, 2008·Genome Biology·Yong ZhangX Shirley Liu
Oct 8, 2009·Genome Biology·Pek S LimMary F Shannon
Nov 10, 2009·Genome Biology·Ana C Marques, Chris P Ponting
Apr 7, 2009·Genome Biology·Paul Flicek
Apr 21, 2009·Genome Biology·Altuna AkalinBoris Lenhard
Dec 25, 2010·Genome Biology·Geir K SandveEivind Hovig
Jun 30, 2010·Genome Biology·Daniel S DayPeter V Kharchenko
Jul 14, 2010·Genome Biology·Rebecca A ChodroffChris P Ponting
Jan 15, 2011·Genome Biology·Shaun MahonyDavid K Gifford
Nov 16, 2011·Genome Biology·Michael F MelgarPraveen Sethupathy
Jan 25, 2012·Genome Biology·Noboru Jo SakabeMarcelo A Nobrega
Oct 26, 2012·Genome Biology·Alexander Meissner
Oct 5, 2012·Genome Biology·Rita RebolloDixie L Mager
Oct 5, 2012·Genome Biology·John P ThomsonRichard R Meehan
Sep 7, 2012·Genome Biology·Xianjun DongZhiping Weng
Jan 31, 2013·Genome Biology·Jong Kyoung Kim, John C Marioni
Jun 6, 2009·Genome Medicine·Christopher G Bell, Stephan Beck
Oct 2, 2012·Journal of Leukocyte Biology·Hoainam T Nguyen-JacksonStephanie S Watowich
Oct 26, 2010·Endocrine Reviews·Z HochbergK Albertsson-Wikland
May 2, 2009·Molecular Endocrinology·Susan C Wu, Yi Zhang
Mar 31, 2010·Molecular Endocrinology·Tiffany G BredfeldtCheryl L Walker