Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae.

The exact lengths of linker DNAs connecting adjacent nucleosomes specify the intrinsic three-dimensional structures of eukaryotic chromatin fibers. Some studies suggest that linker DNA lengths preferentially occur at certain quantized values, differing one from another by integral multiples of the D...

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Autores principales:	Ji-Ping Wang, Yvonne Fondufe-Mittendorf, Liqun Xi, Guei-Feng Tsai, Eran Segal, Jonathan Widom
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2008
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/d08dd766d0724327925944c18868ee8c
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spelling	oai:doaj.org-article:d08dd766d0724327925944c18868ee8c2021-11-25T05:41:59ZPreferentially quantized linker DNA lengths in Saccharomyces cerevisiae.1553-734X1553-735810.1371/journal.pcbi.1000175https://doaj.org/article/d08dd766d0724327925944c18868ee8c2008-09-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/18787693/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358The exact lengths of linker DNAs connecting adjacent nucleosomes specify the intrinsic three-dimensional structures of eukaryotic chromatin fibers. Some studies suggest that linker DNA lengths preferentially occur at certain quantized values, differing one from another by integral multiples of the DNA helical repeat, approximately 10 bp; however, studies in the literature are inconsistent. Here, we investigate linker DNA length distributions in the yeast Saccharomyces cerevisiae genome, using two novel methods: a Fourier analysis of genomic dinucleotide periodicities adjacent to experimentally mapped nucleosomes and a duration hidden Markov model applied to experimentally defined dinucleosomes. Both methods reveal that linker DNA lengths in yeast are preferentially periodic at the DNA helical repeat ( approximately 10 bp), obeying the forms 10n+5 bp (integer n). This 10 bp periodicity implies an ordered superhelical intrinsic structure for the average chromatin fiber in yeast.Ji-Ping WangYvonne Fondufe-MittendorfLiqun XiGuei-Feng TsaiEran SegalJonathan WidomPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 4, Iss 9, p e1000175 (2008)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Ji-Ping Wang Yvonne Fondufe-Mittendorf Liqun Xi Guei-Feng Tsai Eran Segal Jonathan Widom Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae.
description	The exact lengths of linker DNAs connecting adjacent nucleosomes specify the intrinsic three-dimensional structures of eukaryotic chromatin fibers. Some studies suggest that linker DNA lengths preferentially occur at certain quantized values, differing one from another by integral multiples of the DNA helical repeat, approximately 10 bp; however, studies in the literature are inconsistent. Here, we investigate linker DNA length distributions in the yeast Saccharomyces cerevisiae genome, using two novel methods: a Fourier analysis of genomic dinucleotide periodicities adjacent to experimentally mapped nucleosomes and a duration hidden Markov model applied to experimentally defined dinucleosomes. Both methods reveal that linker DNA lengths in yeast are preferentially periodic at the DNA helical repeat ( approximately 10 bp), obeying the forms 10n+5 bp (integer n). This 10 bp periodicity implies an ordered superhelical intrinsic structure for the average chromatin fiber in yeast.
format	article
author	Ji-Ping Wang Yvonne Fondufe-Mittendorf Liqun Xi Guei-Feng Tsai Eran Segal Jonathan Widom
author_facet	Ji-Ping Wang Yvonne Fondufe-Mittendorf Liqun Xi Guei-Feng Tsai Eran Segal Jonathan Widom
author_sort	Ji-Ping Wang
title	Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae.
title_short	Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae.
title_full	Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae.
title_fullStr	Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae.
title_full_unstemmed	Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae.
title_sort	preferentially quantized linker dna lengths in saccharomyces cerevisiae.
publisher	Public Library of Science (PLoS)
publishDate	2008
url	https://doaj.org/article/d08dd766d0724327925944c18868ee8c
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_version_	1718414546049171456

Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae.

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