SKIP Is a Component of the Spliceosome Linking Alternative Splicing and the Circadian Clock in Arabidopsis

Abstract

Circadian clocks generate endogenous rhythms in most organisms from cyanobacteria to humans and facilitate entrainment to environmental diurnal cycles, thus conferring a fitness advantage. Both transcriptional and posttranslational mechanisms are prominent in the basic network architecture of circadian systems. Posttranscriptional regulation, including mRNA processing, is emerging as a critical step for clock function. However, little is known about the molecular mechanisms linking RNA metabolism to the circadian clock network. Here, we report that a conserved SNW/Ski-interacting protein (SKIP) domain protein, SKIP, a splicing factor and component of the spliceosome, is involved in posttranscriptional regulation of circadian clock genes in Arabidopsis thaliana. Mutation in SKIP lengthens the circadian period in a temperature-sensitive manner and affects light input and the sensitivity of the clock to light resetting. SKIP physically interacts with the spliceosomal splicing factor Ser/Arg-rich protein45 and associates with the pre-mRNA of clock genes, such as PSEUDORESPONSE REGULATOR7 (PRR7) and PRR9, and is necessary for the regulation of their alternative splicing and mRNA maturation. Genome-wide investigations reveal that SKIP functions in regulating alternative splicing of many genes, presumably through modulating recognition or cleavage of 59 and 39 splice donor and acceptor sites. Our study addresses a fundamental question on how the mRNA splicing machinery contributes to circadian clock function at a posttranscriptional level.

Unraveling the circadian clock inArabidopsis

“…93 These findings indicate the roles of the splicing factors AtSKIP and STIPL1 in regulating alternative splicing and the period length of the circadian clock. 92,93 A similar phenomenon has been discovered in other organisms. The period gene, which encodes a key component of the circadian oscillator in Drosophila melanogaster, generates two transcripts, type A and type B', in vivo, which differ by an alternatively spliced intron in their 3'-UTRs.…”

“…89 The involvement of splicing factors such as Ski-interacting protein (SKIP) and SPLICEOSOMAL TIMEKEEPER LOCUS1 (STIPL1) in the regulation of the circadian clock in Arabidopsis has also been demonstrated recently. 92,93 Mutations in AtSKIP and STIPL1 increase the period length of the circadian clock. The capacity for temperature compensation is disrupted in skip-1.…”

“…AtSKIP is a conserved SNW domain-containing protein and confirmed component of the spliceosome that associates with the splicing factor SR45; this is consistent with the role of SKIP in both mammals and yeast (Prp45). 62,92,[94][95][96] As a splicing factor, AtSKIP exhibits splicing activity and can complement the defects in the cell cycle, temperature sensitivity and alternative splicing seen in the yeast mutant prp45 (1-169); moreover, mutations in AtSKIP can compromise splice site selection and alter genome-wide splicing patterns. 92,96 AtSKIP is also known to play a pivotal role in the pre-mRNA splicing of several circadian oscillator genes, including PRR7 and PRR9, through direct pre-mRNA binding.…”

“…92,96 AtSKIP is also known to play a pivotal role in the pre-mRNA splicing of several circadian oscillator genes, including PRR7 and PRR9, through direct pre-mRNA binding. 92 …”

“…53,54 A circadian phosphorylation pattern has also been in the alternative splicing of PRR7 and PRR9 partially contribute to lengthening of the circadian period in the skip-1 mutant. 92 STIPL1 is a homolog of the spliceosomal proteins TUFTELIN-INTERACTING PROTEIN11 (TFIP11) in humans and Ntr1p in yeast, which are involved in spliceosome disassembly. 93,97 The mutation of STIPL1 causes less efficient splicing of most of the introns analyzed.…”