Proteins that bind regulatory regions identified by histone modification chromatin immunoprecipitations and mass spectrometry

• DOI: 10.1038/ncomms8155
• Publication Date: 2015-05-20T11:50:23Z
• Authors: Erik Engelen; Johannes H. Brandsma; Maaike J. Moen; Luca Signorile; Dick H. W. Dekkers; Jeroen Demmers; Christel E. M. Kockx; Zehila Ozgür; Wilfred F. J. van...; Debbie L. C. van ...; Raymond A. Poot
• Keywords: Reprogramming; Chromatin immunoprecipitation

The locations of transcriptional enhancers and promoters were recently mapped in many mammalian cell types. Proteins that bind those regulatory regions can determine identity but have not been systematically identified. Here we purify native enhancers, or heterochromatin from embryonic stem cells by chromatin immunoprecipitations (ChIP) for characteristic histone modifications identify associated proteins using mass spectrometry (MS). 239 factors are identified predicted to with different levels activity, heterochromatin. Published genome-wide data indicate a high accuracy location prediction ChIP-MS. A quarter the important pluripotency includes Oct4, Esrrb, Klf5, Mycn Dppa2, drive reprogramming pluripotent cells. We determined binding sites Dppa2 find operates outside classical network. Our ChIP-MS method provides detailed read-out landscape representative investigated type.