Regulation of the nucleosome repeat length in vivo by the DNA sequence, protein concentrations and long-range interactions.

The nucleosome repeat length (NRL) is an integral chromatin property important for its biological functions. Recent experiments revealed several conflicting trends of the NRL dependence on the concentrations of histones and other architectural chromatin proteins, both in vitro and in vivo, but a sys...

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Autores principales:	Daria A Beshnova, Andrey G Cherstvy, Yevhen Vainshtein, Vladimir B Teif
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/ebc23174d96d495bb57b84d82629d730
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spelling	oai:doaj.org-article:ebc23174d96d495bb57b84d82629d7302021-11-25T05:40:59ZRegulation of the nucleosome repeat length in vivo by the DNA sequence, protein concentrations and long-range interactions.1553-734X1553-735810.1371/journal.pcbi.1003698https://doaj.org/article/ebc23174d96d495bb57b84d82629d7302014-07-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24992723/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358The nucleosome repeat length (NRL) is an integral chromatin property important for its biological functions. Recent experiments revealed several conflicting trends of the NRL dependence on the concentrations of histones and other architectural chromatin proteins, both in vitro and in vivo, but a systematic theoretical description of NRL as a function of DNA sequence and epigenetic determinants is currently lacking. To address this problem, we have performed an integrative biophysical and bioinformatics analysis in species ranging from yeast to frog to mouse where NRL was studied as a function of various parameters. We show that in simple eukaryotes such as yeast, a lower limit for the NRL value exists, determined by internucleosome interactions and remodeler action. For higher eukaryotes, also the upper limit exists since NRL is an increasing but saturating function of the linker histone concentration. Counterintuitively, smaller H1 variants or non-histone architectural proteins can initiate larger effects on the NRL due to entropic reasons. Furthermore, we demonstrate that different regimes of the NRL dependence on histone concentrations exist depending on whether DNA sequence-specific effects dominate over boundary effects or vice versa. We consider several classes of genomic regions with apparently different regimes of the NRL variation. As one extreme, our analysis reveals that the period of oscillations of the nucleosome density around bound RNA polymerase coincides with the period of oscillations of positioning sites of the corresponding DNA sequence. At another extreme, we show that although mouse major satellite repeats intrinsically encode well-defined nucleosome preferences, they have no unique nucleosome arrangement and can undergo a switch between two distinct types of nucleosome positioning.Daria A BeshnovaAndrey G CherstvyYevhen VainshteinVladimir B TeifPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 10, Iss 7, p e1003698 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Daria A Beshnova Andrey G Cherstvy Yevhen Vainshtein Vladimir B Teif Regulation of the nucleosome repeat length in vivo by the DNA sequence, protein concentrations and long-range interactions.
description	The nucleosome repeat length (NRL) is an integral chromatin property important for its biological functions. Recent experiments revealed several conflicting trends of the NRL dependence on the concentrations of histones and other architectural chromatin proteins, both in vitro and in vivo, but a systematic theoretical description of NRL as a function of DNA sequence and epigenetic determinants is currently lacking. To address this problem, we have performed an integrative biophysical and bioinformatics analysis in species ranging from yeast to frog to mouse where NRL was studied as a function of various parameters. We show that in simple eukaryotes such as yeast, a lower limit for the NRL value exists, determined by internucleosome interactions and remodeler action. For higher eukaryotes, also the upper limit exists since NRL is an increasing but saturating function of the linker histone concentration. Counterintuitively, smaller H1 variants or non-histone architectural proteins can initiate larger effects on the NRL due to entropic reasons. Furthermore, we demonstrate that different regimes of the NRL dependence on histone concentrations exist depending on whether DNA sequence-specific effects dominate over boundary effects or vice versa. We consider several classes of genomic regions with apparently different regimes of the NRL variation. As one extreme, our analysis reveals that the period of oscillations of the nucleosome density around bound RNA polymerase coincides with the period of oscillations of positioning sites of the corresponding DNA sequence. At another extreme, we show that although mouse major satellite repeats intrinsically encode well-defined nucleosome preferences, they have no unique nucleosome arrangement and can undergo a switch between two distinct types of nucleosome positioning.
format	article
author	Daria A Beshnova Andrey G Cherstvy Yevhen Vainshtein Vladimir B Teif
author_facet	Daria A Beshnova Andrey G Cherstvy Yevhen Vainshtein Vladimir B Teif
author_sort	Daria A Beshnova
title	Regulation of the nucleosome repeat length in vivo by the DNA sequence, protein concentrations and long-range interactions.
title_short	Regulation of the nucleosome repeat length in vivo by the DNA sequence, protein concentrations and long-range interactions.
title_full	Regulation of the nucleosome repeat length in vivo by the DNA sequence, protein concentrations and long-range interactions.
title_fullStr	Regulation of the nucleosome repeat length in vivo by the DNA sequence, protein concentrations and long-range interactions.
title_full_unstemmed	Regulation of the nucleosome repeat length in vivo by the DNA sequence, protein concentrations and long-range interactions.
title_sort	regulation of the nucleosome repeat length in vivo by the dna sequence, protein concentrations and long-range interactions.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/ebc23174d96d495bb57b84d82629d730
work_keys_str_mv	AT dariaabeshnova regulationofthenucleosomerepeatlengthinvivobythednasequenceproteinconcentrationsandlongrangeinteractions AT andreygcherstvy regulationofthenucleosomerepeatlengthinvivobythednasequenceproteinconcentrationsandlongrangeinteractions AT yevhenvainshtein regulationofthenucleosomerepeatlengthinvivobythednasequenceproteinconcentrationsandlongrangeinteractions AT vladimirbteif regulationofthenucleosomerepeatlengthinvivobythednasequenceproteinconcentrationsandlongrangeinteractions
_version_	1718414552903712768

Regulation of the nucleosome repeat length in vivo by the DNA sequence, protein concentrations and long-range interactions.

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