scholarly journals Enhancer Trapping Reveals Widespread Circadian Clock Transcriptional Control in Arabidopsis

2003 ◽  
Vol 132 (2) ◽  
pp. 629-639 ◽  
Author(s):  
Todd P. Michael ◽  
C. Robertson McClung
Keyword(s):  
Circadian Clock ◽  
Transcriptional Control ◽  
Enhancer Trapping

scholarly journals Critical role of deadenylation in regulating poly(A) rhythms and circadian gene expression

2019 ◽  
Author(s):  
Xiangyu Yao ◽  
Shihoko Kojima ◽  
Jing Chen
Keyword(s):  
Gene Expression ◽  
Circadian Clock ◽  
Transcriptional Control ◽  
Critical Role ◽  
Tail Length ◽  
Circadian Gene ◽  
Gene Expression Control ◽  
Rhythmic Gene ◽  
Transcriptional Controls

AbstractThe mammalian circadian clock is deeply rooted in rhythmic regulation of gene expression. Rhythmic transcriptional control mediated by the circadian transcription factors is thought to be the main driver of mammalian circadian gene expression. However, mounting evidence has demonstrated the importance of rhythmic post-transcriptional controls, and it remains unclear how the transcriptional and post-transcriptional mechanisms collectively control rhythmic gene expression. A recent study discovered rhythmicity in poly(A) tail length in mouse liver and its strong correlation with protein expression rhythms. To understand the role of rhythmic poly(A) regulation in circadian gene expression, we constructed a parsimonious model that depicts rhythmic control imposed upon basic mRNA expression and poly(A) regulation processes, including transcription, deadenylation, polyadenylation, and degradation. The model results reveal the rhythmicity in deadenylation as the strongest contributor to the rhythmicity in poly(A) tail length and the rhythmicity in the abundance of the mRNA subpopulation with long poly(A) tails (a rough proxy for mRNA translatability). In line with this finding, the model further shows that the experimentally observed distinct peak phases in the expression of deadenylases, regardless of other rhythmic controls, can robustly group the rhythmic mRNAs by their peak phases in poly(A) tail length and in abundance of the subpopulation with long poly(A) tails. This provides a potential mechanism to synchronize the phases of target gene expression regulated by the same deadenylases. Our findings highlight the critical role of rhythmic deadenylation in regulating poly(A) rhythms and circadian gene expression.Author SummaryThe biological circadian clock regulates various bodily functions such that they anticipate and respond to the day-and-night cycle. To achieve this, the circadian clock controls rhythmic gene expression, and these genes ultimately drive the rhythmicity of downstream biological processes. As a mechanism of driving circadian gene expression, rhythmic transcriptional control has attracted the central focus. However, mounting evidence has also demonstrated the importance of rhythmic post-transcriptional controls. Here we use mathematical modeling to investigate how transcriptional and post-transcriptional rhythms coordinately control rhythmic gene expression. We have particularly focused on rhythmic regulation of the length of poly(A) tail, a nearly universal feature of mRNAs that controls mRNA stability and translation. Our model reveals that the rhythmicity of deadenylation, the process that shortens the poly(A) tail, is the dominant contributor to the rhythmicity in poly(A) tail length and mRNA translatability. Particularly, the phase of deadenylation nearly overrides the other rhythmic processes in controlling the phases of poly(A) tail length and mRNA translatability. Our finding highlights the critical role of rhythmic deadenylation in circadian gene expression control.

scholarly journals Transcriptional Control of Antioxidant Defense by the Circadian Clock

2014 ◽  
Vol 20 (18) ◽  
pp. 2997-3006 ◽  
Author(s):  
Sonal A. Patel ◽  
Nikkhil S. Velingkaar ◽  
Roman V. Kondratov
Keyword(s):  
Circadian Clock ◽  
Transcriptional Control ◽  
Antioxidant Defense

scholarly journals Post-transcriptional control of the mammalian circadian clock: implications for health and disease

2016 ◽  
Vol 468 (6) ◽  
pp. 983-991 ◽  
Author(s):  
Marco Preußner ◽  
Florian Heyd
Keyword(s):  
Circadian Clock ◽  
Transcriptional Control ◽  
Health And Disease

scholarly journals Genome and time-of-day transcriptome of Wolffia australiana link morphological extreme minimization with un-gated plant growth

2020 ◽  
Author(s):  
Todd P. Michael ◽  
Evan Ernst ◽  
Nolan Hartwick ◽  
Philomena Chu ◽  
Douglas Bryant ◽  
...  
Keyword(s):  
Gene Expression ◽  
Circadian Clock ◽  
Transcriptional Control ◽  
Time Course ◽  
Time Of Day ◽  
Transcriptional Networks ◽  
Light Signaling ◽  
Reduced Body ◽  
Carbon Processing ◽  
Reference Genomes

AbstractWolffia is the fastest growing plant genus on Earth with a recorded doubling time of less than a day. Wolffia has a dramatically reduced body plan, primarily growing through a continuous, budding-type asexual reproduction with no obvious phase transition. Most plants are bound by the 24-hour light-dark cycle with the majority of processes such as gene expression partitioned or phased to a specific time-of-day (TOD). However, the role that TOD information and the circadian clock plays in facilitating the growth of a fast-growing plant is unknown. Here we generated draft reference genomes for Wolffia australiana (Benth.) Hartog & Plas to monitor gene expression over a two-day time course under light-dark cycles. Wolffia australiana has the smallest genome size in the genus at 357 Mb and has a dramatically reduced gene set at 15,312 with a specific loss of root (WOX5), vascular (CASP), circadian (TOC1), and light-signaling (NPH3) genes. Remarkably, it has also lost all but one of the NLR genes that are known to be involved in innate immunity. In addition, only 13% of its genes cycle, which is far less than in other plants, with an overrepresentation of genes associated with carbon processing and chloroplast-related functions. Despite having a focused set of cycling genes, TOD cis-elements are conserved in W. australiana, consistent with the overall conservation of transcriptional networks. In contrast to the model plants Arabidopsis thaliana and Oryza sativa, the reduction in cycling genes correlates with fewer pathways under TOD control in Wolffia, which could reflect a release of functional gating. Since TOD networks and the circadian clock work to gate activities to specific times of day, this minimization of regulation may enable Wolffia to grow continuously with optimal economy. Wolffia is an ideal model to study the transcriptional control of growth and the findings presented here could serve as a template for plant improvement.

scholarly journals Direct Transcriptional Control of a p38 MAPK Pathway by the Circadian Clock in Neurospora crassa

PLoS ONE ◽  
2011 ◽  
Vol 6 (11) ◽  
pp. e27149 ◽  
Author(s):  
Teresa M. Lamb ◽  
Charles S. Goldsmith ◽  
Lindsay Bennett ◽  
Katelyn E. Finch ◽  
Deborah Bell-Pedersen
Keyword(s):  
Circadian Clock ◽  
Neurospora Crassa ◽  
P38 Mapk ◽  
Transcriptional Control ◽  
Mapk Pathway ◽  
P38 Mapk Pathway

scholarly journals Circadian clock dysfunction in human omental fat links obesity to metabolic inflammation

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Eleonore Maury ◽  
Benoit Navez ◽  
Sonia M. Brichard
Keyword(s):  
Adipose Tissue ◽  
Circadian Clock ◽  
Transcriptional Control ◽  
Target Genes ◽  
Human Adipose Tissue ◽  
Metabolic Inflammation ◽  
Genome Wide ◽  
Obesity In Mice ◽  
Adipose Tissue Remodeling ◽  
Omental Fat

AbstractTo unravel the pathogenesis of obesity and its complications, we investigate the interplay between circadian clocks and NF-κB pathway in human adipose tissue. The circadian clock function is impaired in omental fat from obese patients. ChIP-seq analyses reveal that the core clock activator, BMAL1 binds to several thousand target genes. NF-κB competes with BMAL1 for transcriptional control of some targets and overall, BMAL1 chromatin binding occurs in close proximity to NF-κB consensus motifs. Obesity relocalizes BMAL1 occupancy genome-wide in human omental fat, thereby altering the transcription of numerous target genes involved in metabolic inflammation and adipose tissue remodeling. Eventually, clock dysfunction appears at early stages of obesity in mice and is corrected, together with impaired metabolism, by NF-κB inhibition. Collectively, our results reveal a relationship between NF-κB and the molecular clock in adipose tissue, which may contribute to obesity-related complications.

Review for "The SNARE Regulator Complexin3 is a Target of the Cone Circadian Clock"

2020 ◽  
Author(s):  
Gianluca Tosini
Keyword(s):  
Circadian Clock

Nutrient-regulated gene expression in eukaryotes

2006 ◽  
Vol 73 ◽  
pp. 85-96 ◽  
Author(s):  
Richard J. Reece ◽  
Laila Beynon ◽  
Stacey Holden ◽  
Amanda D. Hughes ◽  
Karine Rébora ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcriptional Control ◽  
Direct Interaction ◽  
Signalling Pathways ◽  
A Cell ◽  
One Step ◽  
Higher Eukaryotes ◽  
Regulated Gene Expression

The recognition of changes in environmental conditions, and the ability to adapt to these changes, is essential for the viability of cells. There are numerous well characterized systems by which the presence or absence of an individual metabolite may be recognized by a cell. However, the recognition of a metabolite is just one step in a process that often results in changes in the expression of whole sets of genes required to respond to that metabolite. In higher eukaryotes, the signalling pathway between metabolite recognition and transcriptional control can be complex. Recent evidence from the relatively simple eukaryote yeast suggests that complex signalling pathways may be circumvented through the direct interaction between individual metabolites and regulators of RNA polymerase II-mediated transcription. Biochemical and structural analyses are beginning to unravel these elegant genetic control elements.

Sign in / Sign up

Export Citation Format

Share Document