title: Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants.
abstract: Conserved noncoding sequences (CNSs) in DNA are reliable pointers to regulatory elements controlling gene expression. Using a comparative genomics approach with four dicotyledonous plant species (Arabidopsis thaliana, papaya [Carica papaya], poplar [Populus trichocarpa], and grape [Vitis vinifera]), we detected hundreds of CNSs upstream of Arabidopsis genes. Distinct positioning, length, and enrichment for transcription factor binding sites suggest these CNSs play a functional role in transcriptional regulation. The enrichment of transcription factors within the set of genes associated with CNS is consistent with the hypothesis that together they form part of a conserved transcriptional network whose function is to regulate other transcription factors and control development. We identified a set of promoters where regulatory mechanisms are likely to be shared between the model organism Arabidopsis and other dicots, providing areas of focus for further research.
authors.affiliation: Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom.
authors.forename: Laura
authors.initials: L
authors.lastname: Baxter
authors.forename: Aleksey
authors.initials: A
authors.lastname: Jironkin
authors.forename: Richard
authors.initials: R
authors.lastname: Hickman
authors.forename: Jay
authors.initials: J
authors.lastname: Moore
authors.forename: Christopher
authors.initials: C
authors.lastname: Barrington
authors.forename: Peter
authors.initials: P
authors.lastname: Krusche
authors.forename: Nigel P
authors.initials: NP
authors.lastname: Dyer
authors.forename: Vicky
authors.initials: V
authors.lastname: Buchanan-Wollaston
authors.forename: Alexander
authors.initials: A
authors.lastname: Tiskin
authors.forename: Jim
authors.initials: J
authors.lastname: Beynon
authors.forename: Katherine
authors.initials: K
authors.lastname: Denby
authors.forename: Sascha
authors.initials: S
authors.lastname: Ott
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D001665:Binding Sites; D029441:Carica / Q000235:genetics*; D017124:Conserved Sequence; D018744:DNA, Plant / Q000737:chemistry*; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D023281:Genomics; D009707:Nucleosomes / Q000378:metabolism; D032107:Populus / Q000235:genetics*; D017422:Sequence Analysis, DNA; D012984:Software; D027843:Vitis / Q000235:genetics*
chemical_list: D018744:DNA, Plant; D009707:Nucleosomes