title: Genome-Wide Prediction and Validation of Intergenic Enhancers in Arabidopsis Using Open Chromatin Signatures.
abstract: Enhancers are important regulators of gene expression in eukaryotes. Enhancers function independently of their distance and orientation to the promoters of target genes. Thus, enhancers have been difficult to identify. Only a few enhancers, especially distant intergenic enhancers, have been identified in plants. We developed an enhancer prediction system based exclusively on the DNase I hypersensitive sites (DHSs) in the Arabidopsis thaliana genome. A set of 10,044 DHSs located in intergenic regions, which are away from any gene promoters, were predicted to be putative enhancers. We examined the functions of 14 predicted enhancers using the β-glucuronidase gene reporter. Ten of the 14 (71%) candidates were validated by the reporter assay. We also designed 10 constructs using intergenic sequences that are not associated with DHSs, and none of these constructs showed enhancer activities in reporter assays. In addition, the tissue specificity of the putative enhancers can be precisely predicted based on DNase I hypersensitivity data sets developed from different plant tissues. These results suggest that the open chromatin signature-based enhancer prediction system developed in Arabidopsis may serve as a universal system for enhancer identification in plants.
authors.affiliation: Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706 Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Zhu
authors.affiliation: Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706.
authors.forename: Wenli
authors.initials: W
authors.lastname: Zhang
authors.affiliation: Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706.
authors.forename: Tao
authors.identifier: http://orcid.org/0000-0002-7897-0205
authors.initials: T
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China.
authors.forename: Bao
authors.identifier: http://orcid.org/0000-0001-5481-1675
authors.initials: B
authors.lastname: Liu
authors.affiliation: Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706 jjiang1@wisc.edu.
authors.forename: Jiming
authors.initials: J
authors.lastname: Jiang
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D002843:Chromatin / Q000235:genetics* / Q000378:metabolism / Q000648:ultrastructure; D004269:DNA, Bacterial; D021901:DNA, Intergenic; D003850:Deoxyribonuclease I / Q000378:metabolism; D004742:Enhancer Elements, Genetic; D035264:Flowers / Q000235:genetics; D017930:Genes, Reporter; D018745:Genome, Plant; D005966:Glucuronidase / Q000235:genetics; D006657:Histones / Q000378:metabolism; D018515:Plant Leaves / Q000235:genetics; D030821:Plants, Genetically Modified; D022661:RNA, Untranslated / Q000378:metabolism; D015203:Reproducibility of Results
chemical_list: D002843:Chromatin; D004269:DNA, Bacterial; D021901:DNA, Intergenic; D006657:Histones; D022661:RNA, Untranslated; C036483:T-DNA; D003850:Deoxyribonuclease I; D005966:Glucuronidase