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High Nucleosome Occupancy Is Encoded at Human Regulatory Sequences

Active eukaryotic regulatory sites are characterized by open chromatin, and yeast promoters and transcription factor binding sites (TFBSs) typically have low intrinsic nucleosome occupancy. Here, we show that in contrast to yeast, DNA at human promoters, enhancers, and TFBSs generally encodes high i...

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Autores principales: Tillo, Desiree, Kaplan, Noam, Moore, Irene K., Fondufe-Mittendorf, Yvonne, Gossett, Andrea J., Field, Yair, Lieb, Jason D., Widom, Jonathan, Segal, Eran, Hughes, Timothy R.
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2817738/
https://www.ncbi.nlm.nih.gov/pubmed/20161746
http://dx.doi.org/10.1371/journal.pone.0009129
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author Tillo, Desiree
Kaplan, Noam
Moore, Irene K.
Fondufe-Mittendorf, Yvonne
Gossett, Andrea J.
Field, Yair
Lieb, Jason D.
Widom, Jonathan
Segal, Eran
Hughes, Timothy R.
author_facet Tillo, Desiree
Kaplan, Noam
Moore, Irene K.
Fondufe-Mittendorf, Yvonne
Gossett, Andrea J.
Field, Yair
Lieb, Jason D.
Widom, Jonathan
Segal, Eran
Hughes, Timothy R.
author_sort Tillo, Desiree
collection PubMed
description Active eukaryotic regulatory sites are characterized by open chromatin, and yeast promoters and transcription factor binding sites (TFBSs) typically have low intrinsic nucleosome occupancy. Here, we show that in contrast to yeast, DNA at human promoters, enhancers, and TFBSs generally encodes high intrinsic nucleosome occupancy. In most cases we examined, these elements also have high experimentally measured nucleosome occupancy in vivo. These regions typically have high G+C content, which correlates positively with intrinsic nucleosome occupancy, and are depleted for nucleosome-excluding poly-A sequences. We propose that high nucleosome preference is directly encoded at regulatory sequences in the human genome to restrict access to regulatory information that will ultimately be utilized in only a subset of differentiated cells.
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spelling pubmed-28177382010-02-17 High Nucleosome Occupancy Is Encoded at Human Regulatory Sequences Tillo, Desiree Kaplan, Noam Moore, Irene K. Fondufe-Mittendorf, Yvonne Gossett, Andrea J. Field, Yair Lieb, Jason D. Widom, Jonathan Segal, Eran Hughes, Timothy R. PLoS One Research Article Active eukaryotic regulatory sites are characterized by open chromatin, and yeast promoters and transcription factor binding sites (TFBSs) typically have low intrinsic nucleosome occupancy. Here, we show that in contrast to yeast, DNA at human promoters, enhancers, and TFBSs generally encodes high intrinsic nucleosome occupancy. In most cases we examined, these elements also have high experimentally measured nucleosome occupancy in vivo. These regions typically have high G+C content, which correlates positively with intrinsic nucleosome occupancy, and are depleted for nucleosome-excluding poly-A sequences. We propose that high nucleosome preference is directly encoded at regulatory sequences in the human genome to restrict access to regulatory information that will ultimately be utilized in only a subset of differentiated cells. Public Library of Science 2010-02-09 /pmc/articles/PMC2817738/ /pubmed/20161746 http://dx.doi.org/10.1371/journal.pone.0009129 Text en Tillo et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Tillo, Desiree
Kaplan, Noam
Moore, Irene K.
Fondufe-Mittendorf, Yvonne
Gossett, Andrea J.
Field, Yair
Lieb, Jason D.
Widom, Jonathan
Segal, Eran
Hughes, Timothy R.
High Nucleosome Occupancy Is Encoded at Human Regulatory Sequences
title High Nucleosome Occupancy Is Encoded at Human Regulatory Sequences
title_full High Nucleosome Occupancy Is Encoded at Human Regulatory Sequences
title_fullStr High Nucleosome Occupancy Is Encoded at Human Regulatory Sequences
title_full_unstemmed High Nucleosome Occupancy Is Encoded at Human Regulatory Sequences
title_short High Nucleosome Occupancy Is Encoded at Human Regulatory Sequences
title_sort high nucleosome occupancy is encoded at human regulatory sequences
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2817738/
https://www.ncbi.nlm.nih.gov/pubmed/20161746
http://dx.doi.org/10.1371/journal.pone.0009129
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