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PlantDHS: a database for DNase I hypersensitive sites in plants

Gene expression is regulated by orchestrated binding of regulatory proteins to promoters and other cis-regulatory DNA elements (CREs). Several plant databases have been developed for mapping promoters or DNA motifs associated with promoters. However, there is a lack of databases that allow investiga...

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Autores principales: Zhang, Tao, Marand, Alexandre P., Jiang, Jiming
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702941/
https://www.ncbi.nlm.nih.gov/pubmed/26400163
http://dx.doi.org/10.1093/nar/gkv962
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author Zhang, Tao
Marand, Alexandre P.
Jiang, Jiming
author_facet Zhang, Tao
Marand, Alexandre P.
Jiang, Jiming
author_sort Zhang, Tao
collection PubMed
description Gene expression is regulated by orchestrated binding of regulatory proteins to promoters and other cis-regulatory DNA elements (CREs). Several plant databases have been developed for mapping promoters or DNA motifs associated with promoters. However, there is a lack of databases that allow investigation for all CREs. Here we present PlantDHS (http://plantdhs.org), a plant DNase I hypersensitive site (DHS) database that integrates histone modification, RNA sequencing, nucleosome positioning/occupancy, transcription factor binding sites, and genomic sequence within an easily navigated user interface. DHSs are indicative of all CREs, including promoters, enhancers, silencers, insulators and transcription factor binding sites; all of which play immense roles in global gene expression regulation. PlantDHS provides a platform to predict all CREs associated with individual genes from three model plant species, including Arabidopsis thaliana, Brachypodium distachyon and rice (Oryza sativa). PlantDHS is especially valuable in the detection of distant CREs that are located away from promoters.
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spelling pubmed-47029412016-01-07 PlantDHS: a database for DNase I hypersensitive sites in plants Zhang, Tao Marand, Alexandre P. Jiang, Jiming Nucleic Acids Res Database Issue Gene expression is regulated by orchestrated binding of regulatory proteins to promoters and other cis-regulatory DNA elements (CREs). Several plant databases have been developed for mapping promoters or DNA motifs associated with promoters. However, there is a lack of databases that allow investigation for all CREs. Here we present PlantDHS (http://plantdhs.org), a plant DNase I hypersensitive site (DHS) database that integrates histone modification, RNA sequencing, nucleosome positioning/occupancy, transcription factor binding sites, and genomic sequence within an easily navigated user interface. DHSs are indicative of all CREs, including promoters, enhancers, silencers, insulators and transcription factor binding sites; all of which play immense roles in global gene expression regulation. PlantDHS provides a platform to predict all CREs associated with individual genes from three model plant species, including Arabidopsis thaliana, Brachypodium distachyon and rice (Oryza sativa). PlantDHS is especially valuable in the detection of distant CREs that are located away from promoters. Oxford University Press 2016-01-04 2015-09-22 /pmc/articles/PMC4702941/ /pubmed/26400163 http://dx.doi.org/10.1093/nar/gkv962 Text en © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Database Issue
Zhang, Tao
Marand, Alexandre P.
Jiang, Jiming
PlantDHS: a database for DNase I hypersensitive sites in plants
title PlantDHS: a database for DNase I hypersensitive sites in plants
title_full PlantDHS: a database for DNase I hypersensitive sites in plants
title_fullStr PlantDHS: a database for DNase I hypersensitive sites in plants
title_full_unstemmed PlantDHS: a database for DNase I hypersensitive sites in plants
title_short PlantDHS: a database for DNase I hypersensitive sites in plants
title_sort plantdhs: a database for dnase i hypersensitive sites in plants
topic Database Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702941/
https://www.ncbi.nlm.nih.gov/pubmed/26400163
http://dx.doi.org/10.1093/nar/gkv962
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