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Nat Commun. 2015 May 20;6:7155. doi: 10.1038/ncomms8155.

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

Author information

1
Department of Cell Biology, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands.
2
Proteomics Center, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.
3
Center for Biomics, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.
4
1] Department of Cell Biology, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands [2] Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK.

Abstract

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.

PMID:
25990348
PMCID:
PMC4455091
DOI:
10.1038/ncomms8155
[Indexed for MEDLINE]
Free PMC Article
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