Post-transcriptional control of circadian rhythms

Abstract

Circadian rhythms exist in most living organisms. The general molecular mechanisms that are used to generate 24-hour rhythms are conserved among organisms, although the details vary. These core clocks consist of multiple regulatory feedback loops, and must be coordinated and orchestrated appropriately for the fine-tuning of the 24-hour period. Many levels of regulation are important for the proper functioning of the circadian clock, including transcriptional, post-transcriptional and post-translational mechanisms. In recent years, new information about post-transcriptional regulation in the circadian system has been discovered. Such regulation has been shown to alter the phase and amplitude of rhythmic mRNA and protein expression in many organisms. Therefore, this Commentary will provide an overview of current knowledge of post-transcriptional regulation of the clock genes and clock-controlled genes in dinoflagellates, plants, fungi and animals. This article will also highlight how circadian gene expression is modulated by post-transcriptional mechanisms and how this is crucial for robust circadian rhythmicity.

Fig. 1.

Circadian clocks and their contribution to post-transcriptional events. (A) The circadian system is generally considered to comprise three major components: input, oscillator and output. Light is the most powerful input signal, but other cues, such as temperature and nutrient availability, are also used. Examples of output include hormone secretion, body temperature, metabolic activity, sleep and wake cycle (mammals), eclosion, locomotor activity, olfactory responses (Drosophila), conidiation, carbon and nitrogen metabolism (Neurospora), flowering, germination, leaf movement and photosynthesis (Arabidopsis). (B) The generic structure of the molecular clock. Heterodimeric positive regulators (blue and green) activate the expression of negative regulators (purple and pink) by binding cis-regulatory elements in their promoters. Upon translation, these negative regulators inhibit their own transcription by blocking the activity of the positive regulators to complete the cycle. This cycle takes about 24 hours and thus generates circadian oscillation. Positive regulators also activate transcription of ccgs to drive rhythmic gene expression and generate circadian output. (C) The involvement of circadian rhythms in post-transcriptional regulation. Red oscillators indicate the steps that are known to be regulated by circadian clocks. Green, yellow and red arrows indicate pathways leading towards translation, translational silencing and mRNA degradation pathways, respectively. ^m7Gppp, 7-methylguanosine cap.

Fig. 2.

The effect of light on post-transcriptional regulation of clock genes in Arabidopsis. Light is perceived by photoreceptors (PHYB, red light; CRY1 and CRY2; blue light) and this input signal is transmitted to the circadian core loop to entrain the clock. ZTL is also a blue-light photoreceptor, affecting an evening loop, and regulates TOC1 expression together with GIGANTEA (GI). Light also provokes several post-transcriptional events, such as CCA1 mRNA degradation, translational activation of LHY and the enhancement of the amplitude of TOC1 rhythmic expression. PRR7 and PRR9 are PSEUDO RESPONSE REGULATOR 7 and PSEUDO RESPONSE REGULATOR 9.

Fig. 3.

Post-transcriptional control of mammalian clock genes. (A) The regulation of Cry1 or Per2 mRNA stability by hnRNP D or I (hnD/I). During the night-time, the expression of hnRNP proteins in the cytoplasm is relatively high and more Cry1 and Per2 mRNAs are subject to degradation, leading to lower levels of mRNA (relative RNA levels depicted by curves on the left). By contrast, the level of hnRNPs is relatively low during the day; therefore, both Cry1 and Per2 mRNA can escape from the degradation caused by hnRNPs. Thus, these mRNAs become more stable, leading to higher mRNA levels. (B) Post-transcriptional and post-translational regulation of AANAT protein expression. During the night-time, hnRNP Q (hnQ) expression increases and this promotes the translation of AANAT through the interaction with IRESs. AANAT protein is phosphorylated by a PKA-mediated pathway and this prevents it from being degraded by the proteasome. Both of these post-transcriptional and post-translational regulatory steps contribute to the extreme amplitude of AANAT expression during the night. At the same time, hnRNP Q also binds to the 3′-UTR of Aanat mRNA and promotes degradation of Aanat mRNA. During the day, Aanat mRNA expression and the level of cytoplasmic hnRNP Q are low, and little or no AANAT protein is made. Melatonin is synthesized from tryptophan by four enzymatic steps, of which AANAT catalyzes the third to convert serotonin to N-acetylserotonin. The effects of hnRNP L and hnRNP R are not depicted here for simplicity. ^m7Gppp, 7-methylguanosine cap.

Fig. 4.

Temperature-regulated alternative splicing of clock genes. (A) Temperature-sensitive splicing of frq. At low temperature, splicing at the non-canonical splice sites becomes dominant, leading to higher levels of expression of short-FRQ (sFRQ). At higher temperature, the canonical splicing site dominates, leading to higher levels of long-FRQ (l-FRQ) expression. (B) Temperature-sensitive splicing of Drosophila Per. There are two transcript forms of Per; one includes an intron sequence in the 3′-UTR and the other does not. Even though this difference does not alter the protein structure of PER, this splicing promotes the earlier accumulation of Per and PER, and advances the evening locomotor activity of fly. This might be a mechanism for adjustment to winter time, in which the temperature is lower and the photoperiod is shorter. (C) Autoregulation of AtGRP7 and AtGRP8 expression. AtGRP7 and AtGRP8 mRNAs are both induced by cold temperature. The protein level of AtGRP7, but not AtGRP8, is also increased by the cold temperature. Both AtGRP7 and AtGRP8 interact with their pre-mRNA, and promote the splicing that yields aberrant mRNA. As a consequence, these abnormal RNAs are degraded rapidly in the cell.