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

The locations of transcriptional enhancers and promoters were recently mapped in many mammalian cell types. Proteins that bind those regulatory regions can determine cell identity but have not been systematically identified. Here we purify native enhancers, promoters or heterochromatin from embryoni...

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Bibliographic Details
Published in:	Nature communications Vol. 6; no. 1; p. 7155
Main Authors:	Engelen, Erik, Brandsma, Johannes H., Moen, Maaike J., Signorile, Luca, Dekkers, Dick H. W., Demmers, Jeroen, Kockx, Christel E. M., Ozgür, Zehila, van IJcken, Wilfred F. J., van den Berg, Debbie L. C., Poot, Raymond A.
Format:	Journal Article
Language:	English
Published:	London Nature Publishing Group UK 20-05-2015 Nature Publishing Group Nature Pub. Group
Subjects:	631/136/532/2064/2117 631/1647/2217/2088 631/1647/296 631/208/726/2102 82 82/58 Animals Binding Sites Catalytic Domain Chromatin Immunoprecipitation - methods Embryonic Stem Cells - cytology Enhancer Elements, Genetic Genome Histone Code Histones - chemistry Humanities and Social Sciences Kruppel-Like Transcription Factors - chemistry Mass Spectrometry - methods Mice multidisciplinary N-Myc Proto-Oncogene Protein Nuclear Proteins - chemistry Octamer Transcription Factor-3 - metabolism Pluripotent Stem Cells - cytology Promoter Regions, Genetic Protein Binding Proto-Oncogene Proteins - chemistry Receptors, Estrogen - chemistry Regulatory Sequences, Nucleic Acid Reproducibility of Results Science Science (multidisciplinary)
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Summary:	The locations of transcriptional enhancers and promoters were recently mapped in many mammalian cell types. Proteins that bind those regulatory regions can determine cell identity but have not been systematically identified. Here we purify native enhancers, promoters or heterochromatin from embryonic stem cells by chromatin immunoprecipitations (ChIP) for characteristic histone modifications and identify associated proteins using mass spectrometry (MS). 239 factors are identified and predicted to bind enhancers or promoters with different levels of activity, or heterochromatin. Published genome-wide data indicate a high accuracy of location prediction by ChIP-MS. A quarter of the identified factors are important for pluripotency and includes Oct4, Esrrb, Klf5, Mycn and Dppa2, factors that drive reprogramming to pluripotent stem cells. We determined the genome-wide binding sites of Dppa2 and find that Dppa2 operates outside the classical pluripotency network. Our ChIP-MS method provides a detailed read-out of the transcriptional landscape representative of the investigated cell type. The protein factors that bind to regulatory regions in the genome have not been systematically mapped. Here the authors performed chromatin immunoprecipitations for histone modifications associated with promoters, enhancers or heterochromatin in mouse embryonic stem cells and assigned a genome location to many factors important for pluripotency.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 These authors contributed equally to this work
ISSN:	2041-1723 2041-1723
DOI:	10.1038/ncomms8155