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.
Bibliographical noteFunding 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 We thank R. Sherwood (Harvard University) for sharing unpublished observations and T Jessell (Columbia University) for anti-Hoxc4 antibody.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.).