title: Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays.
abstract: BACKGROUND
  Organisms are able to anticipate changes in the daily environment with an internal oscillator know as the circadian clock. Transcription is an important mechanism in maintaining these oscillations. Here we explore, using whole genome tiling arrays, the extent of rhythmic expression patterns genome-wide, with an unbiased analysis of coding and noncoding regions of the Arabidopsis genome.
  
  
  RESULTS
  As in previous studies, we detected a circadian rhythm for approximately 25% of the protein coding genes in the genome. With an unbiased interrogation of the genome, extensive rhythmic introns were detected predominantly in phase with adjacent rhythmic exons, creating a transcript that, if translated, would be expected to produce a truncated protein. In some cases, such as the MYB transcription factor AT2G20400, an intron was found to exhibit a circadian rhythm while the remainder of the transcript was otherwise arrhythmic. In addition to several known noncoding transcripts, including microRNA, trans-acting short interfering RNA, and small nucleolar RNA, greater than one thousand intergenic regions were detected as circadian clock regulated, many of which have no predicted function, either coding or noncoding. Nearly 7% of the protein coding genes produced rhythmic antisense transcripts, often for genes whose sense strand was not similarly rhythmic.
  
  
  CONCLUSIONS
  This study revealed widespread circadian clock regulation of the Arabidopsis genome extending well beyond the protein coding transcripts measured to date. This suggests a greater level of structural and temporal dynamics than previously known.
authors.affiliation: Section of Cell and Developmental Biology, University of California San Diego, Gilman Drive, La Jolla, CA 92093-0130, USA.
authors.forename: Samuel P
authors.initials: SP
authors.lastname: Hazen
authors.forename: Felix
authors.initials: F
authors.lastname: Naef
authors.forename: Tom
authors.initials: T
authors.lastname: Quisel
authors.forename: Joshua M
authors.initials: JM
authors.lastname: Gendron
authors.forename: Huaming
authors.initials: H
authors.lastname: Chen
authors.forename: Joseph R
authors.initials: JR
authors.lastname: Ecker
authors.forename: Justin O
authors.initials: JO
authors.lastname: Borevitz
authors.forename: Steve A
authors.initials: SA
authors.lastname: Kay
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D002940:Circadian Rhythm / Q000235:genetics*; D005091:Exons; D020869:Gene Expression Profiling / Q000379:methods; D018506:Gene Expression Regulation, Plant / Q000502:physiology*; D018745:Genome, Plant / Q000235:genetics*; D007438:Introns; D022661:RNA, Untranslated; D014158:Transcription, Genetic
chemical_list: D022661:RNA, Untranslated