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CpG island-mediated global gene regulatory modes in mouse embryonic stem cells

Both transcriptional and epigenetic regulations are fundamental for the control of eukaryotic gene expression. Here we perform a compendium analysis of >200 large sequencing data sets to elucidate the regulatory logic of global gene expression programs in mouse embryonic stem (ES) cells. We defin...

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Detalles Bibliográficos
Autores principales: Beck, Samuel, Lee, Bum-Kyu, Rhee, Catherine, Song, Jawon, Woo, Andrew J., Kim, Jonghwan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Pub. Group 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4236720/
https://www.ncbi.nlm.nih.gov/pubmed/25405324
http://dx.doi.org/10.1038/ncomms6490
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author Beck, Samuel
Lee, Bum-Kyu
Rhee, Catherine
Song, Jawon
Woo, Andrew J.
Kim, Jonghwan
author_facet Beck, Samuel
Lee, Bum-Kyu
Rhee, Catherine
Song, Jawon
Woo, Andrew J.
Kim, Jonghwan
author_sort Beck, Samuel
collection PubMed
description Both transcriptional and epigenetic regulations are fundamental for the control of eukaryotic gene expression. Here we perform a compendium analysis of >200 large sequencing data sets to elucidate the regulatory logic of global gene expression programs in mouse embryonic stem (ES) cells. We define four major classes of DNA-binding proteins (Core, PRC, MYC and CTCF) based on their target co-occupancy, and discover reciprocal regulation between the MYC and PRC classes for the activity of nearly all genes under the control of the CpG island (CGI)-containing promoters. This CGI-dependent regulatory mode explains the functional segregation between CGI-containing and CGI-less genes during early development. By defining active enhancers based on the co-occupancy of the Core class, we further demonstrate their additive roles in CGI-containing gene expression and cell type-specific roles in CGI-less gene expression. Altogether, our analyses provide novel insights into previously unknown CGI-dependent global gene regulatory modes.
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spelling pubmed-42367202014-12-05 CpG island-mediated global gene regulatory modes in mouse embryonic stem cells Beck, Samuel Lee, Bum-Kyu Rhee, Catherine Song, Jawon Woo, Andrew J. Kim, Jonghwan Nat Commun Article Both transcriptional and epigenetic regulations are fundamental for the control of eukaryotic gene expression. Here we perform a compendium analysis of >200 large sequencing data sets to elucidate the regulatory logic of global gene expression programs in mouse embryonic stem (ES) cells. We define four major classes of DNA-binding proteins (Core, PRC, MYC and CTCF) based on their target co-occupancy, and discover reciprocal regulation between the MYC and PRC classes for the activity of nearly all genes under the control of the CpG island (CGI)-containing promoters. This CGI-dependent regulatory mode explains the functional segregation between CGI-containing and CGI-less genes during early development. By defining active enhancers based on the co-occupancy of the Core class, we further demonstrate their additive roles in CGI-containing gene expression and cell type-specific roles in CGI-less gene expression. Altogether, our analyses provide novel insights into previously unknown CGI-dependent global gene regulatory modes. Nature Pub. Group 2014-11-18 /pmc/articles/PMC4236720/ /pubmed/25405324 http://dx.doi.org/10.1038/ncomms6490 Text en Copyright © 2014, 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
Beck, Samuel
Lee, Bum-Kyu
Rhee, Catherine
Song, Jawon
Woo, Andrew J.
Kim, Jonghwan
CpG island-mediated global gene regulatory modes in mouse embryonic stem cells
title CpG island-mediated global gene regulatory modes in mouse embryonic stem cells
title_full CpG island-mediated global gene regulatory modes in mouse embryonic stem cells
title_fullStr CpG island-mediated global gene regulatory modes in mouse embryonic stem cells
title_full_unstemmed CpG island-mediated global gene regulatory modes in mouse embryonic stem cells
title_short CpG island-mediated global gene regulatory modes in mouse embryonic stem cells
title_sort cpg island-mediated global gene regulatory modes in mouse embryonic stem cells
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4236720/
https://www.ncbi.nlm.nih.gov/pubmed/25405324
http://dx.doi.org/10.1038/ncomms6490
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