RNA around the clock - regulation at the RNA level in biological timing

Abstract

The circadian timing system in plants synchronizes their physiological functions with the environment. This is achieved by a global control of gene expression programs with a considerable part of the transcriptome undergoing 24-h oscillations in steady-state abundance. These circadian oscillations are driven by a set of core clock proteins that generate their own 24-h rhythm through periodic feedback on their own transcription. Additionally, post-transcriptional events are instrumental for oscillations of core clock genes and genes in clock output. Here we provide an update on molecular events at the RNA level that contribute to the 24-h rhythm of the core clock proteins and shape the circadian transcriptome. We focus on the circadian system of the model plant Arabidopsis thaliana but also discuss selected regulatory principles in other organisms.

Keywords: RNA-binding protein; circadian oscillation; post-transcriptional regulation.

FIGURE 1

Steps in pre-mRNA processing. See text for details.

FIGURE 2

Scheme of the Arabidopsis core clockwork. In the central loop LHY and CCA1 on the one hand and TOC1 on the other hand reciprocally repress their own expression. In the morning loop, LHY and CCA1 activate PRR9 and PRR7 which in turn repress CCA1 and LHY. PRR7 and PRR9 expression is switched off during the night through the EC consisting of LUX, EFL3, and ELF4. In the evening loop, the EC and TOC1 reciprocally regulate their expression.

FIGURE 3

Types of alternative splicing events. (A) Exon skipping (B) alternative 5′ splice site (C) alternative 3′ splice site (D) intron retention. Blue boxes: exons; green boxes: alternative exons; lines: introns; solid diagonal lines: constitutive splicing events; broken diagonal lines: alternative splicing events.

FIGURE 4

Alternative splicing events in core clock genes. The scheme of the genes are shown on the top of each panel, the fully spliced isoforms encoding the full length proteins are indicated on the left side and alternative splice isoforms are indicated on the right side. (A) CCA1. The fully spliced isoform encoding full length CCA1 [designated CCA1α by Seo et al. (2012)] is indicated on the left. The splice isoform with intron 4 retained is shown on the right. It is predicted to encode a polypeptide terminating at the PTC within intron 4, thus comprising only the DNA-binding Myb domain, or the CCA1β polypeptide comprising only the dimerization domain (Seo et al., 2012). (B) LHY. The splice isoform with alternative splicing at intron 5 leading to inclusion of exon 5a including a PTC is shown on the right. (C) PRR9. The splice isoform retaining intron 3 including a PTC is shown on the right (black broken arrow). The spliced isoform with additional eight nucleotides at exon 2 due to the use of an alternative 5′ splice site entailing a frame shift is shown on the right at the bottom (red broken line). This splice isoform is elevated in prmt5.

FIGURE 5

A clock-regulated negative autoregulatory circuit based on alternative splicing and NMD. In response to increasing AtGRP7 levels the use of the cryptic intronic 5′ splice site is favored, leading to unproductive splicing with the splice isoform being degraded via NMD.

FIGURE 6

Post-transcriptional processes in the Arabidopsis circadian system. Numerous core clock genes undergo alternative splicing, in particular in response to temperature changes. The spliceosomal Lsm4 and Lsm5 proteins control alternatives splicing. PRMT5 affects alternative splicing of core clock genes likely through modification of snRNP proteins and splicing factors. Alternative splice isoforms of clock genes containing a PTC can undergo NMD. The RNA-binding proteins AtGRP7 and AtGRP8 are part of a clock-controlled post-transcriptional feedback loop based on alternative splicing and NMD. Translation of the core clock component LHY is regulated. The stability of LHCB1 and CCL is time-of-day dependent. CCA1 stability depends on the light quality. Some miRNA show diurnal oscillations. Several pri-miRNAs undergo clock-controlled oscillations. See text for further details.