title: Embryonic stem cell-based mapping of developmental transcriptional programs.
abstract: The study of developmentally regulated transcription factors by chromatin immunoprecipitation and deep sequencing (ChIP-seq) faces two major obstacles: availability of ChIP-grade antibodies and access to sufficient number of cells. We describe versatile genome-wide analysis of transcription-factor binding sites by combining directed differentiation of embryonic stem cells and inducible expression of tagged proteins. We demonstrate its utility by mapping DNA-binding sites of transcription factors involved in motor neuron specification.
authors.affiliation: Departments of Pathology, Neurology and Neuroscience, Center for Motor Neuron Biology and Disease and Columbia Stem Cell Initiative, Columbia University Medical Center, New York, New York, USA.
authors.forename: Esteban O
authors.initials: EO
authors.lastname: Mazzoni
authors.forename: Shaun
authors.initials: S
authors.lastname: Mahony
authors.forename: Michelina
authors.initials: M
authors.lastname: Iacovino
authors.forename: Carolyn A
authors.initials: CA
authors.lastname: Morrison
authors.forename: George
authors.initials: G
authors.lastname: Mountoufaris
authors.forename: Michael
authors.initials: M
authors.lastname: Closser
authors.forename: Warren A
authors.initials: WA
authors.lastname: Whyte
authors.forename: Richard A
authors.initials: RA
authors.lastname: Young
authors.forename: Michael
authors.initials: M
authors.lastname: Kyba
authors.forename: David K
authors.initials: DK
authors.lastname: Gifford
authors.forename: Hynek
authors.initials: H
authors.lastname: Wichterle
mesh_terms: D000818:Animals; D002454:Cell Differentiation / Q000235:genetics; D047369:Chromatin Immunoprecipitation; D004268:DNA-Binding Proteins / Q000378:metabolism; D053595:Embryonic Stem Cells / Q000166:cytology* / Q000378:metabolism*; D018507:Gene Expression Regulation, Developmental; D055106:Genome-Wide Association Study; D059014:High-Throughput Nucleotide Sequencing; D051379:Mice; D009046:Motor Neurons / Q000166:cytology / Q000378:metabolism; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D004268:DNA-Binding Proteins; D014157:Transcription Factors
references.citation: Bioinformatics. 2011 Jan 15;27(2):270-1
references.pmid: 21081511
references.citation: Genome Biol. 2009;10(3):R25
references.pmid: 19261174
references.citation: Neuron. 2011 Feb 24;69(4):721-35
references.pmid: 21338882
references.citation: Proc Natl Acad Sci U S A. 2006 Jan 31;103(5):1551-6
references.pmid: 16432183
references.citation: Nat Rev Genet. 2009 Oct;10(10):669-80
references.pmid: 19736561
references.citation: Neuron. 2001 Sep 13;31(5):773-89
references.pmid: 11567616
references.citation: Neuron. 2010 Sep 9;67(5):781-96
references.pmid: 20826310
references.citation: Curr Protoc Stem Cell Biol. 2009 Mar;Chapter 1:Unit1B.5
references.pmid: 19306258
references.citation: Nat Rev Genet. 2000 Oct;1(1):20-9
references.pmid: 11262869
references.citation: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W253-8
references.pmid: 17478497
references.citation: Stem Cells. 2011 Oct;29(10):1580-8
references.pmid: 22039605
references.citation: Bioinformatics. 2010 Dec 15;26(24):3028-34
references.pmid: 20966006
references.citation: Nat Protoc. 2009;4(4):506-17
references.pmid: 19325547
references.citation: Cell. 2002 Aug 9;110(3):385-97
references.pmid: 12176325