Embryonic stem cell-based mapping of developmental transcriptional programs

Esteban O. Mazzoni, Shaun Mahony, Michelina Iacovino, Carolyn A. Morrison, George Mountoufaris, Michael Closser, Warren A. Whyte, Richard A. Young, Michael Kyba, David K. Gifford, Hynek Wichterle

Research output: Contribution to journalArticlepeer-review

57 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)1056-1060
Number of pages5
JournalNature Methods
Issue number12
StatePublished - Dec 2011

Bibliographical note

Funding Information:
E.O.M. is funded as the David and Sylvia Lieb Fellow of the Damon Runyon Cancer Research Foundation (DRG-1937-07). We thank R. Sherwood (Harvard University) for sharing unpublished observations and T Jessell (Columbia University) for anti-Hoxc4 antibody. Personnel and work were supported by US National Institutes of Health grant P01 NS055923 (D.K.G., R.A.Y. and H.W.), R01 NS058502 (H.W.), R01HL081186 (M.K.) and Helmsley Stem Cell Starter grant (H.W.).


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