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Are nucleosome positions in vivo primarily determined by histone–DNA sequence preferences?

Large-scale and genome-wide studies have concluded that ∼80% of the yeast (Saccharomyces cerevisiae) genome is occupied by positioned nucleosomes. In vivo this nucleosome organization can result from a variety of mechanisms, including the intrinsic DNA sequence preferences for wrapping the DNA aroun...

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Detalles Bibliográficos
Autores principales: Stein, Arnold, Takasuka, Taichi E., Collings, Clayton K.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2817465/
https://www.ncbi.nlm.nih.gov/pubmed/19934265
http://dx.doi.org/10.1093/nar/gkp1043
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author Stein, Arnold
Takasuka, Taichi E.
Collings, Clayton K.
author_facet Stein, Arnold
Takasuka, Taichi E.
Collings, Clayton K.
author_sort Stein, Arnold
collection PubMed
description Large-scale and genome-wide studies have concluded that ∼80% of the yeast (Saccharomyces cerevisiae) genome is occupied by positioned nucleosomes. In vivo this nucleosome organization can result from a variety of mechanisms, including the intrinsic DNA sequence preferences for wrapping the DNA around the histone core. Recently, a genome-wide study was reported using massively parallel sequencing to directly compare in vivo and in vitro nucleosome positions. It was concluded that intrinsic DNA sequence preferences indeed have a dominant role in determining the in vivo nucleosome organization of the genome, consistent with a genomic code for nucleosome positioning. Some other studies disagree with this view. Using the large amount of data now available from several sources, we have attempted to clarify a fundamental question concerning the packaging of genomic DNA: to what extent are nucleosome positions in vivo determined by histone-DNA sequence preferences? We have analyzed data obtained from different laboratories in the same way, and have directly compared these data. We also identify possible problems with some of the experimental designs used and with the data analysis. Our findings suggest that DNA sequence preferences have only small effects on the positioning of individual nucleosomes throughout the genome in vivo.
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spelling pubmed-28174652010-02-08 Are nucleosome positions in vivo primarily determined by histone–DNA sequence preferences? Stein, Arnold Takasuka, Taichi E. Collings, Clayton K. Nucleic Acids Res Survey and Summary Large-scale and genome-wide studies have concluded that ∼80% of the yeast (Saccharomyces cerevisiae) genome is occupied by positioned nucleosomes. In vivo this nucleosome organization can result from a variety of mechanisms, including the intrinsic DNA sequence preferences for wrapping the DNA around the histone core. Recently, a genome-wide study was reported using massively parallel sequencing to directly compare in vivo and in vitro nucleosome positions. It was concluded that intrinsic DNA sequence preferences indeed have a dominant role in determining the in vivo nucleosome organization of the genome, consistent with a genomic code for nucleosome positioning. Some other studies disagree with this view. Using the large amount of data now available from several sources, we have attempted to clarify a fundamental question concerning the packaging of genomic DNA: to what extent are nucleosome positions in vivo determined by histone-DNA sequence preferences? We have analyzed data obtained from different laboratories in the same way, and have directly compared these data. We also identify possible problems with some of the experimental designs used and with the data analysis. Our findings suggest that DNA sequence preferences have only small effects on the positioning of individual nucleosomes throughout the genome in vivo. Oxford University Press 2010-01 2009-11-24 /pmc/articles/PMC2817465/ /pubmed/19934265 http://dx.doi.org/10.1093/nar/gkp1043 Text en © The Author(s) 2009. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Survey and Summary
Stein, Arnold
Takasuka, Taichi E.
Collings, Clayton K.
Are nucleosome positions in vivo primarily determined by histone–DNA sequence preferences?
title Are nucleosome positions in vivo primarily determined by histone–DNA sequence preferences?
title_full Are nucleosome positions in vivo primarily determined by histone–DNA sequence preferences?
title_fullStr Are nucleosome positions in vivo primarily determined by histone–DNA sequence preferences?
title_full_unstemmed Are nucleosome positions in vivo primarily determined by histone–DNA sequence preferences?
title_short Are nucleosome positions in vivo primarily determined by histone–DNA sequence preferences?
title_sort are nucleosome positions in vivo primarily determined by histone–dna sequence preferences?
topic Survey and Summary
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2817465/
https://www.ncbi.nlm.nih.gov/pubmed/19934265
http://dx.doi.org/10.1093/nar/gkp1043
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