Transcriptional and post-transcriptional control of the plant circadian gene regulatory network

Abstract

The circadian clock drives rhythms in multiple physiological processes allowing plants to anticipate and adjust to periodic changes in environmental conditions. These physiological rhythms are associated with robust oscillations in the expression of thousands of genes linked to the control of photosynthesis, cell elongation, biotic and abiotic stress responses, developmental processes such as flowering, and the clock itself. Given its pervasive effects on plant physiology, it is not surprising that circadian clock genes have played an important role in the domestication of crop plants and in the improvement of crop productivity. Therefore, identifying the principles governing the dynamics of the circadian gene regulatory network in plants could strongly contribute to further speed up crop improvement. Here we provide an historical as well as a current description of our knowledge of the molecular mechanisms underlying circadian rhythms in plants. This work focuses on the transcriptional and post-transcriptional regulatory layers that control the very core of the circadian clock, and some of its complex interactions with signaling pathways that help synchronize plant growth and development to daily and seasonal changes in the environment. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.

RNA editing in inflorescences of wild grapevine unveils association to sex and development

“…In mammals, recent findings proposed that 3' UTRs may play important roles in the regulation of biological processes (Berkovits and Mayr, 2015), probably due to its engagement in intricate RNA base-pairing patterns, which may change in response to protein binding and impact the recruitment of ribosomes particles (Campbell et al, 2012;Castello et al, 2012) as well as, modulate translation (Mayr, 2017) at the 3' UTR. In plants it is well established that UTRs represent important genetic components controlling gene expression and regulating mRNAs and protein interactions (Hernando et al, 2017;Petrillo et al, 2014). Previous works already suggested that such regulation acts through a wide range of mechanisms that, under diverse cellular conditions, enables a rapid and dynamic response in order to recode gene information (Alvarez et al, 2016;Gallegos and Rose, 2015;Meyer et al, 2015;Yang et al, 2012).…”

Circadian processes in the RNA life cycle

“…Indeed, in most vertebrate species, this mechanism is sustained by interlocked transcriptional-translational feedback loops (TTFL) of activators and repressors that form a canonical positive-feedback and negative-feedback gene network motif (Novák & Tyson, 2008). The TTFL cycle has a period of approximately 24 hr (for reviews, see Cohen & Golden, 2015;Hernando, Romanowski, & Yanovsky, 2017;Hurley, Loros, & Dunlap, 2015;Ozkaya & Rosato, 2012;Takahashi, 2015).…”

From network to phenotype: the dynamic wiring of an Arabidopsis transcriptional network induced by osmotic stress

“…A very well‐known example of a GRN is the circadian clock regulatory network (Nagel & Kay, 2012; Pokhilko et al , 2012; Seaton et al , 2015; Hernando et al , 2017). This network consists of a core oscillator module of three TFs (CIRCADIAN CLOCK ASSOCIATED1 (CCA1), LATE HYPOCOTYL (LHY) and TIMING OF CAB1 (TOC1)) that forms the base of a larger interconnected network regulating circadian rhythms, hypocotyl growth, and flowering of Arabidopsis plants through transcriptional but also post‐translational regulation, chromatin remodeling, and alternative splicing (Nakamichi, 2011; Malapeira et al , 2012; Perez‐Santángelo et al , 2013; Wang & Ma, 2013).…”