Chromatin Dynamics and Transcriptional Control of Circadian Rhythms in Arabidopsis

Abstract

Circadian rhythms pervade nearly all aspects of plant growth, physiology, and development. Generation of the rhythms relies on an endogenous timing system or circadian clock that generates 24-hour oscillations in multiple rhythmic outputs. At its bases, the plant circadian function relies on dynamic interactive networks of clock components that regulate each other to generate rhythms at specific phases during the day and night. From the initial discovery more than 13 years ago of a parallelism between the oscillations in chromatin status and the transcriptional rhythms of an Arabidopsis clock gene, a number of studies have later expanded considerably our view on the circadian epigenome and transcriptome landscapes. Here, we describe the most recent identification of chromatin-related factors that are able to directly interact with Arabidopsis clock proteins to shape the transcriptional waveforms of circadian gene expression and clock outputs. We discuss how changes in chromatin marks associate with transcript initiation, elongation, and the rhythms of nascent RNAs, and speculate on future interesting research directions in the field.

Diurnal RNAPII-tethered chromatin interactions are associated with rhythmic gene expression in rice

“…Diurnal oscillations of gene expression are presumed to drive daily cycles of plant physiological processes through core circadian genes involved in interlocked transcriptional/translational negative feedback loops [1][2][3][4][5][6][7][8]. The genome-wide cis-acting targets (cistromes) of core circadian clock components during the circadian cycle have been identified in mammals using the high-throughput chromatin immunoprecipitation (ChIP) approach [9][10][11].…”

Closing the protein gap in plant chronobiology

“…Our understanding of plant chronobiology and diel plant cell regulation has been significantly enhanced through gene expression studies, driven by the evolution of technologies from single‐gene quantitative PCR (qPCR) to systems‐level tools such as microarrays and RNA sequencing (RNA‐seq) (Maric and Mas, 2020). Time‐course transcriptomics experimentation has provided, and continues to provide, us with a wealth of knowledge of diel gene regulation across a range of organisms, including Arabidopsis (Kamioka et al ., 2016), soybean ( Glycine max ) (Li et al ., 2019), lettuce ( Lactuca sativa ) (Higashi et al ., 2016) and Brassica rapa (Greenham et al ., 2020).…”

Plant clock modifications for adapting flowering time to local environments

“…The starting point was a screening for mutants that change the circadian period of genes fused to a luciferase reporter, followed by identification of the causal genes ( Millar et al, 1995 ). In addition to the forward genetic approaches, reverse genetics, functional genetics, biochemical analyses, mathematical modeling, and chemical–biological investigations have revealed the molecular processes underpinning the Arabidopsis circadian clock ( Nohales and Kay, 2016 ; Creux and Harmer, 2019 ; McClung, 2019 ; Ono et al, 2019 ; Saito et al, 2019 ; Uehara et al, 2019 ; Webb et al, 2019 ; Maric and Mas, 2020 ; Nohales, 2021 ; Yan et al, 2021 ). Also, analyses of mutants impaired in photoperiodic flowering identified core clock genes such as EARLY FLOWERING3 ( ELF3 ), ELF4 , GIGANTEA ( GI ), and LATE ELONGATED HYPOCOTYL ( LHY ) ( Hicks et al, 1996 ; Schaffer et al, 1998 ; Fowler et al, 1999 ; Doyle et al, 2002 ).…”