title: Epigenome analysis of pluripotent stem cells.
abstract: Mis-regulation of gene expression due to epigenetic abnormalities has been linked with complex genetic disorders, psychiatric illness, and cancer. In addition, the dynamic epigenetic changes that occur in pluripotent stem cells are believed to impact regulatory networks essential for proper lineage development. Chromatin immunoprecipitation (ChIP) is a technique used to enrich genomic fragments using antibodies against specific chromatin modifications, such as DNA-binding proteins or modified histones. Until recently, many ChIP protocols required large numbers of cells for each immunoprecipitation. This severely limited analysis of rare cell populations or post-mitotic, differentiated cell lines. Here, we describe a low cell number ChIP protocol with next generation sequencing and analysis that has the potential to uncover novel epigenetic regulatory pathways that were previously difficult or impossible to obtain.
authors.affiliation: Rutgers Stem Cell Research Center, The W.M. Keck Center for Collaborative Neuroscience, Rutgers University, Piscataway, NJ, USA.
authors.forename: Christopher L
authors.initials: CL
authors.lastname: Ricupero
authors.forename: Mavis R
authors.initials: MR
authors.lastname: Swerdel
authors.forename: Ronald P
authors.initials: RP
authors.lastname: Hart
mesh_terms: D000818:Animals; D018929:Cell Culture Techniques; D002478:Cells, Cultured; D047369:Chromatin Immunoprecipitation; D044127:Epigenesis, Genetic; D006657:Histones / Q000378:metabolism; D006801:Humans; D039904:Pluripotent Stem Cells / Q000378:metabolism*; D011499:Protein Processing, Post-Translational; D017422:Sequence Analysis, DNA
chemical_list: D006657:Histones
references.citation: Cell. 2007 Feb 23;128(4):693-705
references.pmid: 17320507
references.citation: Curr Protoc Hum Genet. 2011 Oct;Chapter 18:Unit18.6
references.pmid: 21975940
references.citation: Cell. 1988 Jun 17;53(6):937-47
references.pmid: 2454748
references.citation: Nat Rev Genet. 2009 Oct;10(10):669-80
references.pmid: 19736561
references.citation: Cell Stem Cell. 2008 Mar 6;2(3):230-40
references.pmid: 18371448
references.citation: Cell. 2006 Apr 21;125(2):315-26
references.pmid: 16630819
references.citation: Science. 2000 Dec 22;290(5500):2306-9
references.pmid: 11125145
references.citation: Pediatr Res. 2006 Apr;59(4 Pt 2):21R-5R
references.pmid: 16549544
references.citation: Cell. 2007 Feb 23;128(4):635-8
references.pmid: 17320500
references.citation: Cell. 2007 May 18;129(4):823-37
references.pmid: 17512414
references.citation: Curr Protoc Mol Biol. 2009 Oct;Chapter 19:Unit19.9
references.pmid: 19816931
references.citation: Biochim Biophys Acta. 2008 Aug;1779(8):432-7
references.pmid: 18674649
references.citation: Genes Dev. 2002 Jan 1;16(1):6-21
references.pmid: 11782440
references.citation: Genome Biol. 2009;10(3):R25
references.pmid: 19261174
references.citation: Nat Genet. 2001 Aug;28(4):327-34
references.pmid: 11455386
references.citation: JAMA. 2008 Mar 19;299(11):1345-50
references.pmid: 18349095
references.citation: Cell. 2006 Aug 25;126(4):663-76
references.pmid: 16904174
references.citation: Nat Rev Genet. 2008 Mar;9(3):179-91
references.pmid: 18250624
references.citation: Ann Neurol. 2008 Dec;64(6):602-17
references.pmid: 19107999
references.citation: BMC Bioinformatics. 2010 May 11;11:237
references.pmid: 20459804
references.citation: Cell. 2009 Apr 3;137(1):13-7
references.pmid: 19345179
references.citation: EMBO J. 1988 May;7(5):1395-402
references.pmid: 3409869
references.citation: Nat Methods. 2007 Aug;4(8):651-7
references.pmid: 17558387
references.citation: Nature. 2007 May 24;447(7143):396-8
references.pmid: 17522671
references.citation: Science. 2007 Jun 8;316(5830):1497-502
references.pmid: 17540862
references.citation: Bioinformatics. 2008 Aug 1;24(15):1729-30
references.pmid: 18599518
references.citation: Bioinformatics. 2009 Aug 15;25(16):2078-9
references.pmid: 19505943