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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...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Pub. Group
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4455091/ https://www.ncbi.nlm.nih.gov/pubmed/25990348 http://dx.doi.org/10.1038/ncomms8155 |
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author | 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. |
author_facet | 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. |
author_sort | Engelen, Erik |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-4455091 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Nature Pub. Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-44550912015-06-18 Proteins that bind regulatory regions identified by histone modification chromatin immunoprecipitations and mass spectrometry 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. Nat Commun Article 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. Nature Pub. Group 2015-05-20 /pmc/articles/PMC4455091/ /pubmed/25990348 http://dx.doi.org/10.1038/ncomms8155 Text en Copyright © 2015, Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved. http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ |
spellingShingle | Article 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. Proteins that bind regulatory regions identified by histone modification chromatin immunoprecipitations and mass spectrometry |
title | Proteins that bind regulatory regions identified by histone modification chromatin immunoprecipitations and mass spectrometry |
title_full | Proteins that bind regulatory regions identified by histone modification chromatin immunoprecipitations and mass spectrometry |
title_fullStr | Proteins that bind regulatory regions identified by histone modification chromatin immunoprecipitations and mass spectrometry |
title_full_unstemmed | Proteins that bind regulatory regions identified by histone modification chromatin immunoprecipitations and mass spectrometry |
title_short | Proteins that bind regulatory regions identified by histone modification chromatin immunoprecipitations and mass spectrometry |
title_sort | proteins that bind regulatory regions identified by histone modification chromatin immunoprecipitations and mass spectrometry |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4455091/ https://www.ncbi.nlm.nih.gov/pubmed/25990348 http://dx.doi.org/10.1038/ncomms8155 |
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