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CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters

One clear hallmark of mammalian promoters is the presence of CpG islands (CGIs) at more than two-thirds of genes, whereas TATA boxes are only present at a minority of promoters. Using genome-wide approaches, we show that GC content and CGIs are major promoter elements in mammalian cells, able to gov...

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Autores principales: Fenouil, Romain, Cauchy, Pierre, Koch, Frederic, Descostes, Nicolas, Cabeza, Joaquin Zacarias, Innocenti, Charlène, Ferrier, Pierre, Spicuglia, Salvatore, Gut, Marta, Gut, Ivo, Andrau, Jean-Christophe
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514669/
https://www.ncbi.nlm.nih.gov/pubmed/23100115
http://dx.doi.org/10.1101/gr.138776.112
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author Fenouil, Romain
Cauchy, Pierre
Koch, Frederic
Descostes, Nicolas
Cabeza, Joaquin Zacarias
Innocenti, Charlène
Ferrier, Pierre
Spicuglia, Salvatore
Gut, Marta
Gut, Ivo
Andrau, Jean-Christophe
author_facet Fenouil, Romain
Cauchy, Pierre
Koch, Frederic
Descostes, Nicolas
Cabeza, Joaquin Zacarias
Innocenti, Charlène
Ferrier, Pierre
Spicuglia, Salvatore
Gut, Marta
Gut, Ivo
Andrau, Jean-Christophe
author_sort Fenouil, Romain
collection PubMed
description One clear hallmark of mammalian promoters is the presence of CpG islands (CGIs) at more than two-thirds of genes, whereas TATA boxes are only present at a minority of promoters. Using genome-wide approaches, we show that GC content and CGIs are major promoter elements in mammalian cells, able to govern open chromatin conformation and support paused transcription. First, we define three classes of promoters with distinct transcriptional directionality and pausing properties that correlate with their GC content. We further analyze the direct influence of GC content on nucleosome positioning and depletion and show that CpG content and CGI width correlate with nucleosome depletion both in vivo and in vitro. We also show that transcription is not essential for nucleosome exclusion but influences both a weak +1 and a well-positioned nucleosome at CGI borders. Altogether our data support the idea that CGIs have become an essential feature of promoter structure defining novel regulatory properties in mammals.
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spelling pubmed-35146692013-06-01 CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters Fenouil, Romain Cauchy, Pierre Koch, Frederic Descostes, Nicolas Cabeza, Joaquin Zacarias Innocenti, Charlène Ferrier, Pierre Spicuglia, Salvatore Gut, Marta Gut, Ivo Andrau, Jean-Christophe Genome Res Research One clear hallmark of mammalian promoters is the presence of CpG islands (CGIs) at more than two-thirds of genes, whereas TATA boxes are only present at a minority of promoters. Using genome-wide approaches, we show that GC content and CGIs are major promoter elements in mammalian cells, able to govern open chromatin conformation and support paused transcription. First, we define three classes of promoters with distinct transcriptional directionality and pausing properties that correlate with their GC content. We further analyze the direct influence of GC content on nucleosome positioning and depletion and show that CpG content and CGI width correlate with nucleosome depletion both in vivo and in vitro. We also show that transcription is not essential for nucleosome exclusion but influences both a weak +1 and a well-positioned nucleosome at CGI borders. Altogether our data support the idea that CGIs have become an essential feature of promoter structure defining novel regulatory properties in mammals. Cold Spring Harbor Laboratory Press 2012-12 /pmc/articles/PMC3514669/ /pubmed/23100115 http://dx.doi.org/10.1101/gr.138776.112 Text en © 2012, Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by-nc/3.0/ This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), as described at http://creativecommons.org/licenses/by-nc/3.0/.
spellingShingle Research
Fenouil, Romain
Cauchy, Pierre
Koch, Frederic
Descostes, Nicolas
Cabeza, Joaquin Zacarias
Innocenti, Charlène
Ferrier, Pierre
Spicuglia, Salvatore
Gut, Marta
Gut, Ivo
Andrau, Jean-Christophe
CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters
title CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters
title_full CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters
title_fullStr CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters
title_full_unstemmed CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters
title_short CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters
title_sort cpg islands and gc content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514669/
https://www.ncbi.nlm.nih.gov/pubmed/23100115
http://dx.doi.org/10.1101/gr.138776.112
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