title: The 'dark matter' in the plant genomes: non-coding and unannotated DNA sequences associated with open chromatin.
abstract: Sequencing of complete plant genomes has become increasingly more routine since the advent of the next-generation sequencing technology. Identification and annotation of large amounts of noncoding but functional DNA sequences, including cis-regulatory DNA elements (CREs), have become a new frontier in plant genome research. Genomic regions containing active CREs bound to regulatory proteins are hypersensitive to DNase I digestion and are called DNase I hypersensitive sites (DHSs). Several recent DHS studies in plants illustrate that DHS datasets produced by DNase I digestion followed by next-generation sequencing (DNase-seq) are highly valuable for the identification and characterization of CREs associated with plant development and responses to environmental cues. DHS-based genomic profiling has opened a door to identify and annotate the 'dark matter' in sequenced plant genomes.
authors.affiliation: Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA. Electronic address: jjiang1@wisc.edu.
authors.forename: Jiming
authors.initials: J
authors.lastname: Jiang
mesh_terms: D001483:Base Sequence; D002843:Chromatin / Q000235:genetics* / Q000378:metabolism; D003850:Deoxyribonuclease I / Q000235:genetics* / Q000378:metabolism; D018745:Genome, Plant; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D010944:Plants / Q000235:genetics; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D002843:Chromatin; D010940:Plant Proteins; D014157:Transcription Factors; D003850:Deoxyribonuclease I