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Structural features based genome-wide characterization and prediction of nucleosome organization

BACKGROUND: Nucleosome distribution along chromatin dictates genomic DNA accessibility and thus profoundly influences gene expression. However, the underlying mechanism of nucleosome formation remains elusive. Here, taking a structural perspective, we systematically explored nucleosome formation pot...

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Detalles Bibliográficos
Autores principales: Gan, Yanglan, Guan, Jihong, Zhou, Shuigeng, Zhang, Weixiong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3378464/
https://www.ncbi.nlm.nih.gov/pubmed/22449207
http://dx.doi.org/10.1186/1471-2105-13-49
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author Gan, Yanglan
Guan, Jihong
Zhou, Shuigeng
Zhang, Weixiong
author_facet Gan, Yanglan
Guan, Jihong
Zhou, Shuigeng
Zhang, Weixiong
author_sort Gan, Yanglan
collection PubMed
description BACKGROUND: Nucleosome distribution along chromatin dictates genomic DNA accessibility and thus profoundly influences gene expression. However, the underlying mechanism of nucleosome formation remains elusive. Here, taking a structural perspective, we systematically explored nucleosome formation potential of genomic sequences and the effect on chromatin organization and gene expression in S. cerevisiae. RESULTS: We analyzed twelve structural features related to flexibility, curvature and energy of DNA sequences. The results showed that some structural features such as DNA denaturation, DNA-bending stiffness, Stacking energy, Z-DNA, Propeller twist and free energy, were highly correlated with in vitro and in vivo nucleosome occupancy. Specifically, they can be classified into two classes, one positively and the other negatively correlated with nucleosome occupancy. These two kinds of structural features facilitated nucleosome binding in centromere regions and repressed nucleosome formation in the promoter regions of protein-coding genes to mediate transcriptional regulation. Based on these analyses, we integrated all twelve structural features in a model to predict more accurately nucleosome occupancy in vivo than the existing methods that mainly depend on sequence compositional features. Furthermore, we developed a novel approach, named DLaNe, that located nucleosomes by detecting peaks of structural profiles, and built a meta predictor to integrate information from different structural features. As a comparison, we also constructed a hidden Markov model (HMM) to locate nucleosomes based on the profiles of these structural features. The result showed that the meta DLaNe and HMM-based method performed better than the existing methods, demonstrating the power of these structural features in predicting nucleosome positions. CONCLUSIONS: Our analysis revealed that DNA structures significantly contribute to nucleosome organization and influence chromatin structure and gene expression regulation. The results indicated that our proposed methods are effective in predicting nucleosome occupancy and positions and that these structural features are highly predictive of nucleosome organization. The implementation of our DLaNe method based on structural features is available online.
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spelling pubmed-33784642012-06-20 Structural features based genome-wide characterization and prediction of nucleosome organization Gan, Yanglan Guan, Jihong Zhou, Shuigeng Zhang, Weixiong BMC Bioinformatics Research Article BACKGROUND: Nucleosome distribution along chromatin dictates genomic DNA accessibility and thus profoundly influences gene expression. However, the underlying mechanism of nucleosome formation remains elusive. Here, taking a structural perspective, we systematically explored nucleosome formation potential of genomic sequences and the effect on chromatin organization and gene expression in S. cerevisiae. RESULTS: We analyzed twelve structural features related to flexibility, curvature and energy of DNA sequences. The results showed that some structural features such as DNA denaturation, DNA-bending stiffness, Stacking energy, Z-DNA, Propeller twist and free energy, were highly correlated with in vitro and in vivo nucleosome occupancy. Specifically, they can be classified into two classes, one positively and the other negatively correlated with nucleosome occupancy. These two kinds of structural features facilitated nucleosome binding in centromere regions and repressed nucleosome formation in the promoter regions of protein-coding genes to mediate transcriptional regulation. Based on these analyses, we integrated all twelve structural features in a model to predict more accurately nucleosome occupancy in vivo than the existing methods that mainly depend on sequence compositional features. Furthermore, we developed a novel approach, named DLaNe, that located nucleosomes by detecting peaks of structural profiles, and built a meta predictor to integrate information from different structural features. As a comparison, we also constructed a hidden Markov model (HMM) to locate nucleosomes based on the profiles of these structural features. The result showed that the meta DLaNe and HMM-based method performed better than the existing methods, demonstrating the power of these structural features in predicting nucleosome positions. CONCLUSIONS: Our analysis revealed that DNA structures significantly contribute to nucleosome organization and influence chromatin structure and gene expression regulation. The results indicated that our proposed methods are effective in predicting nucleosome occupancy and positions and that these structural features are highly predictive of nucleosome organization. The implementation of our DLaNe method based on structural features is available online. BioMed Central 2012-03-26 /pmc/articles/PMC3378464/ /pubmed/22449207 http://dx.doi.org/10.1186/1471-2105-13-49 Text en Copyright © 2012 Gan et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Gan, Yanglan
Guan, Jihong
Zhou, Shuigeng
Zhang, Weixiong
Structural features based genome-wide characterization and prediction of nucleosome organization
title Structural features based genome-wide characterization and prediction of nucleosome organization
title_full Structural features based genome-wide characterization and prediction of nucleosome organization
title_fullStr Structural features based genome-wide characterization and prediction of nucleosome organization
title_full_unstemmed Structural features based genome-wide characterization and prediction of nucleosome organization
title_short Structural features based genome-wide characterization and prediction of nucleosome organization
title_sort structural features based genome-wide characterization and prediction of nucleosome organization
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3378464/
https://www.ncbi.nlm.nih.gov/pubmed/22449207
http://dx.doi.org/10.1186/1471-2105-13-49
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