title: PlantDHS: a database for DNase I hypersensitive sites in plants.
abstract: 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.
authors.affiliation: Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Tao
authors.initials: T
authors.lastname: Zhang
authors.affiliation: Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Alexandre P
authors.identifier: http://orcid.org/0000-0002-7897-0205
authors.initials: AP
authors.lastname: Marand
authors.affiliation: Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA jjiang1@wisc.edu.
authors.forename: Jiming
authors.initials: J
authors.lastname: Jiang
mesh_terms: D029681:Arabidopsis Proteins / Q000378:metabolism; D001665:Binding Sites; D030541:Databases, Genetic; D003850:Deoxyribonuclease I; D020869:Gene Expression Profiling; D023281:Genomics; D006657:Histones / Q000378:metabolism; D009707:Nucleosomes / Q000378:metabolism; D010944:Plants / Q000235:genetics* / Q000378:metabolism; D050436:Regulatory Elements, Transcriptional; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D029681:Arabidopsis Proteins; D006657:Histones; D009707:Nucleosomes; D014157:Transcription Factors; C096661:superman protein, Arabidopsis; D003850:Deoxyribonuclease I