The Exosome Regulates Circadian Gene Expression in a Posttranscriptional Negative Feedback Loop

Abstract

Summary The eukaryotic circadian oscillators consist of autoregulatory negative feedback loops. However, little is known about the role of post-transcriptional regulation of RNA in circadian oscillators. In the Neurospora circadian negative feedback loop, FRQ and FRH form the FFC complex that represses frq transcription. Here we show that FFC also binds frq RNA and interacts with the exosome to regulate frq RNA decay. Consequently, frq RNA is robustly rhythmic as it is more stable when FRQ levels are low. Silencing of RRP44, the catalytic subunit of the exosome, elevates frq RNA levels and impairs clock function. In addition, rrp44 is a clock-controlled gene and a direct target of the WHITE COLLAR complex, and RRP44 controls the circadian expression of at least one ccg. Taken together, these results suggest that FFC and the exosome are part of a post-transcriptional negative feedback loop that regulates frq transcript levels and the circadian output pathway.

The RNA helicase FRH is an ATP-dependent regulator of CK1a in the circadian clock of Neurospora crassa

“…It has been suggested that the FFC facilitates rhythmic turnover of frq RNA 14 . The mutant frq 9 allele expresses full-length RNA but, due to a frameshift mutation, it encodes a truncated FRQ 9 protein that does not associate with FRH 14 .…”

“…The mutant frq 9 allele expresses full-length RNA but, due to a frameshift mutation, it encodes a truncated FRQ 9 protein that does not associate with FRH 14 . We inhibited transcription in WT and frq 9 strains with thiolutin 14 and found that the turnover kinetics of frq and frq 9 RNA was similar ( Supplementary Fig. 2a), suggesting that the FFC may not regulate turnover of frq RNA.…”

“…In addition, FRH has been implicated in a variety of non-essential, clock-related functions: FRH is crucial for cytoplasmic localization and turnover of FRQ 15,16 , and also for the interaction of FRQ with the circadian transcription activator White Collar Complex (WCC) 15,17 . Furthermore, it was reported that FRH mediates turnover of frq RNA by committing the messenger for degradation by the exosome 14 . However, molecular mechanisms underlying these functions are not known.…”

“…Mtr4p, the Saccharomyces cerevisiae orthologue of FRH, is a component of the TRAMP complex and regulates RNA metabolism in cooperation with the nuclear exosome [10][11][12][13] . FRH is essential for the viability of Neurospora owing to its function in RNA metabolism 14 . In addition, FRH has been implicated in a variety of non-essential, clock-related functions: FRH is crucial for cytoplasmic localization and turnover of FRQ 15,16 , and also for the interaction of FRQ with the circadian transcription activator White Collar Complex (WCC) 15,17 .…”

Unraveling the circadian clock inArabidopsis

“…[50][51][52] Phosphorylation plays a pivotal role in regulating the activity and abundance of clock components. The abundance of some circadian clock-associated proteins, including LHY, CASEIN KINASE 2B4 (CKB4) and XAP5 CIRCADIAN TIMEKEEPER, is modulated by phosphorylation.…”