Prediction of nucleosome positioning based on transcription factor binding sites.

<h4>Background</h4>The DNA of all eukaryotic organisms is packaged into nucleosomes, the basic repeating units of chromatin. The nucleosome consists of a histone octamer around which a DNA core is wrapped and the linker histone H1, which is associated with linker DNA. By altering the acc...

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Autores principales:	Xianfu Yi, Yu-Dong Cai, Zhisong He, Weiren Cui, Xiangyin Kong
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2010
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/08bf6fdec40a4541afe92e9dfcde8c75
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spelling	oai:doaj.org-article:08bf6fdec40a4541afe92e9dfcde8c752021-11-18T06:35:33ZPrediction of nucleosome positioning based on transcription factor binding sites.1932-620310.1371/journal.pone.0012495https://doaj.org/article/08bf6fdec40a4541afe92e9dfcde8c752010-09-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20824131/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>The DNA of all eukaryotic organisms is packaged into nucleosomes, the basic repeating units of chromatin. The nucleosome consists of a histone octamer around which a DNA core is wrapped and the linker histone H1, which is associated with linker DNA. By altering the accessibility of DNA sequences, the nucleosome has profound effects on all DNA-dependent processes. Understanding the factors that influence nucleosome positioning is of great importance for the study of genomic control mechanisms. Transcription factors (TFs) have been suggested to play a role in nucleosome positioning in vivo.<h4>Principal findings</h4>Here, the minimum redundancy maximum relevance (mRMR) feature selection algorithm, the nearest neighbor algorithm (NNA), and the incremental feature selection (IFS) method were used to identify the most important TFs that either favor or inhibit nucleosome positioning by analyzing the numbers of transcription factor binding sites (TFBSs) in 53,021 nucleosomal DNA sequences and 50,299 linker DNA sequences. A total of nine important families of TFs were extracted from 35 families, and the overall prediction accuracy was 87.4% as evaluated by the jackknife cross-validation test.<h4>Conclusions</h4>Our results are consistent with the notion that TFs are more likely to bind linker DNA sequences than the sequences in the nucleosomes. In addition, our results imply that there may be some TFs that are important for nucleosome positioning but that play an insignificant role in discriminating nucleosome-forming DNA sequences from nucleosome-inhibiting DNA sequences. The hypothesis that TFs play a role in nucleosome positioning is, thus, confirmed by the results of this study.Xianfu YiYu-Dong CaiZhisong HeWeiren CuiXiangyin KongPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 5, Iss 9 (2010)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Xianfu Yi Yu-Dong Cai Zhisong He Weiren Cui Xiangyin Kong Prediction of nucleosome positioning based on transcription factor binding sites.
description	<h4>Background</h4>The DNA of all eukaryotic organisms is packaged into nucleosomes, the basic repeating units of chromatin. The nucleosome consists of a histone octamer around which a DNA core is wrapped and the linker histone H1, which is associated with linker DNA. By altering the accessibility of DNA sequences, the nucleosome has profound effects on all DNA-dependent processes. Understanding the factors that influence nucleosome positioning is of great importance for the study of genomic control mechanisms. Transcription factors (TFs) have been suggested to play a role in nucleosome positioning in vivo.<h4>Principal findings</h4>Here, the minimum redundancy maximum relevance (mRMR) feature selection algorithm, the nearest neighbor algorithm (NNA), and the incremental feature selection (IFS) method were used to identify the most important TFs that either favor or inhibit nucleosome positioning by analyzing the numbers of transcription factor binding sites (TFBSs) in 53,021 nucleosomal DNA sequences and 50,299 linker DNA sequences. A total of nine important families of TFs were extracted from 35 families, and the overall prediction accuracy was 87.4% as evaluated by the jackknife cross-validation test.<h4>Conclusions</h4>Our results are consistent with the notion that TFs are more likely to bind linker DNA sequences than the sequences in the nucleosomes. In addition, our results imply that there may be some TFs that are important for nucleosome positioning but that play an insignificant role in discriminating nucleosome-forming DNA sequences from nucleosome-inhibiting DNA sequences. The hypothesis that TFs play a role in nucleosome positioning is, thus, confirmed by the results of this study.
format	article
author	Xianfu Yi Yu-Dong Cai Zhisong He Weiren Cui Xiangyin Kong
author_facet	Xianfu Yi Yu-Dong Cai Zhisong He Weiren Cui Xiangyin Kong
author_sort	Xianfu Yi
title	Prediction of nucleosome positioning based on transcription factor binding sites.
title_short	Prediction of nucleosome positioning based on transcription factor binding sites.
title_full	Prediction of nucleosome positioning based on transcription factor binding sites.
title_fullStr	Prediction of nucleosome positioning based on transcription factor binding sites.
title_full_unstemmed	Prediction of nucleosome positioning based on transcription factor binding sites.
title_sort	prediction of nucleosome positioning based on transcription factor binding sites.
publisher	Public Library of Science (PLoS)
publishDate	2010
url	https://doaj.org/article/08bf6fdec40a4541afe92e9dfcde8c75
work_keys_str_mv	AT xianfuyi predictionofnucleosomepositioningbasedontranscriptionfactorbindingsites AT yudongcai predictionofnucleosomepositioningbasedontranscriptionfactorbindingsites AT zhisonghe predictionofnucleosomepositioningbasedontranscriptionfactorbindingsites AT weirencui predictionofnucleosomepositioningbasedontranscriptionfactorbindingsites AT xiangyinkong predictionofnucleosomepositioningbasedontranscriptionfactorbindingsites
_version_	1718424395767087104

Prediction of nucleosome positioning based on transcription factor binding sites.

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