title: Alternative splicing mediates responses of the Arabidopsis circadian clock to temperature changes.
abstract: Alternative splicing plays crucial roles by influencing the diversity of the transcriptome and proteome and regulating protein structure/function and gene expression. It is widespread in plants, and alteration of the levels of splicing factors leads to a wide variety of growth and developmental phenotypes. The circadian clock is a complex piece of cellular machinery that can regulate physiology and behavior to anticipate predictable environmental changes on a revolving planet. We have performed a system-wide analysis of alternative splicing in clock components in Arabidopsis thaliana plants acclimated to different steady state temperatures or undergoing temperature transitions. This revealed extensive alternative splicing in clock genes and dynamic changes in alternatively spliced transcripts. Several of these changes, notably those affecting the circadian clock genes late elongated hypocotyl (LHY) and pseudo response regulator7, are temperature-dependent and contribute markedly to functionally important changes in clock gene expression in temperature transitions by producing nonfunctional transcripts and/or inducing nonsense-mediated decay. Temperature effects on alternative splicing contribute to a decline in LHY transcript abundance on cooling, but LHY promoter strength is not affected. We propose that temperature-associated alternative splicing is an additional mechanism involved in the operation and regulation of the plant circadian clock.
authors.affiliation: Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland.
authors.forename: Allan B
authors.initials: AB
authors.lastname: James
authors.forename: Naeem Hasan
authors.initials: NH
authors.lastname: Syed
authors.forename: Simon
authors.initials: S
authors.lastname: Bordage
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Marshall
authors.forename: Gillian A
authors.initials: GA
authors.lastname: Nimmo
authors.forename: Gareth I
authors.initials: GI
authors.lastname: Jenkins
authors.forename: Pawel
authors.initials: P
authors.lastname: Herzyk
authors.forename: John W S
authors.initials: JW
authors.lastname: Brown
authors.forename: Hugh G
authors.initials: HG
authors.lastname: Nimmo
mesh_terms: D017398:Alternative Splicing; D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics; D057906:Circadian Clocks; D004269:DNA, Bacterial / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D016254:Mutagenesis, Insertional; D011401:Promoter Regions, Genetic; D018749:RNA, Plant / Q000235:genetics; D012097:Repressor Proteins; D013696:Temperature; D014157:Transcription Factors / Q000235:genetics; D014158:Transcription, Genetic
chemical_list: D029681:Arabidopsis Proteins; C114425:CCA1 protein, Arabidopsis; D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; C113192:LHY protein, Arabidopsis; C523308:PRR7 protein, Arabidopsis; D018749:RNA, Plant; D012097:Repressor Proteins; C036483:T-DNA; D014157:Transcription Factors