Alternative Splicing Mediates Responses of the Arabidopsis Circadian Clock to Temperature Changes

• Published in: The Plant cell Vol. 24; no. 3; pp. 961 - 981
• Main Authors: James, Allan B, Syed, Naeem Hasan, Bordage, Simon, Marshall, Jacqueline, Nimmo, Gillian A, Jenkins, Gareth I, Herzyk, Pawel, Brown, John W.S, Nimmo, Hugh G
• Format: Journal Article
• Language: English
• Published: England American Society of Plant Biologists 01-03-2012; American Society of Plant Physiologists
• Subjects: Acclimatization; Alternative Splicing; Arabidopsis - genetics; Arabidopsis - metabolism; Arabidopsis Proteins - genetics; Arabidopsis thaliana; Circadian Clocks; circadian rhythm; Circadian rhythms; Cooling; DNA, Bacterial - genetics; DNA-Binding Proteins - genetics; Environmental changes; Exons; gene expression; Gene expression regulation; Gene Expression Regulation, Plant; Genes; growth and development; Introns; Mutagenesis, Insertional; phenotype; Promoter Regions, Genetic; protein structure; proteome; Repressor Proteins; Reverse transcriptase polymerase chain reaction; RNA; RNA, Plant - genetics; Splicing; Temperature; Transcription Factors - genetics; Transcription, Genetic; transcriptome
• ISSN: 1040-4651; 1532-298X
• DOI: 10.1105/tpc.111.093948

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.