Time-course RNASeq of Camponotus floridanus forager and nurse ant brains indicate links between plasticity in the biological clock and behavioral division of labor DOI Creative Commons
Biplabendu Das, Charissa de Bekker

BMC Genomics, Journal Year: 2022, Volume and Issue: 23(1)

Published: Jan. 15, 2022

Circadian clocks allow organisms to anticipate daily fluctuations in their environment by driving rhythms physiology and behavior. Inter-organismal differences rhythms, called chronotypes, exist can shift with age. In ants, age, caste-related behavior chronotype appear be linked. Brood-tending nurse ants are usually younger individuals show "around-the-clock" activity. With age or the absence of brood, nurses transition into foraging that Ants adaptively between these behavioral castes caste-associated chronotypes depending on social context. We investigated how changes gene expression could contributing such plasticity Camponotus floridanus carpenter combining time-course assays RNA-Sequencing forager brains.We found brains have three times fewer 24 h oscillating genes than foragers. However, several hundred oscillated every showed robust 8 oscillations nurses, including core clock Period Shaggy. These differentially rhythmic consisted components circadian entrainment output pathway, said involved regulating insect locomotory also Vitellogenin, known regulate division labor insects, but not Finally, we significant overlap expressed two ant ultradian expression.This study provides a first look at chronobiological brains. This endeavor allowed us identify putative molecular mechanism underlying plastic timekeeping: its seemingly oscillate different harmonics rhythm. propose has evolved for distinct regulatory networks underlie castes, while supporting swift caste transitions response colony demands. Behavioral is common among insects. The links C. floridanus, thus, likely represent more general phenomenon warrants further investigation.

Language: Английский

Effects of Diurnal Variation of Gut Microbes and High-Fat Feeding on Host Circadian Clock Function and Metabolism DOI Creative Commons
Vanessa Leone, Sean M. Gibbons, Kristina Martinez

et al.

Cell Host & Microbe, Journal Year: 2015, Volume and Issue: 17(5), P. 681 - 689

Published: April 17, 2015

Language: Английский

Citations

751
Pancreatic β cell enhancers regulate rhythmic transcription of genes controlling insulin secretion DOI Open Access

Mark Perelis,

Biliana Marcheva, Kathryn Moynihan Ramsey

et al.

Science, Journal Year: 2015, Volume and Issue: 350(6261)

Published: Nov. 5, 2015

The mammalian transcription factors CLOCK and BMAL1 are essential components of the molecular clock that coordinate behavior metabolism with solar cycle. Genetic or environmental perturbation circadian cycles contributes to metabolic disorders including type 2 diabetes. To study impact cell-autonomous on pancreatic β cell function, we examined islets from mice either intact disrupted expression both throughout life limited adulthood. We found pronounced oscillation insulin secretion was synchronized genes encoding secretory machinery signaling regulate release. CLOCK/BMAL1 colocalized factor PDX1 within active enhancers distinct those controlling rhythmic gene networks in liver. also ablation adult caused severe glucose intolerance. Thus, type-specific underlie control peripheral may help explain its dysregulation

Language: Английский

Citations

343
Guidelines for Genome-Scale Analysis of Biological Rhythms DOI Creative Commons
Michael E. Hughes, Katharine C. Abruzzi, Ravi Allada

et al.

Journal of Biological Rhythms, Journal Year: 2017, Volume and Issue: 32(5), P. 380 - 393

Published: Oct. 1, 2017

Genome biology approaches have made enormous contributions to our understanding of biological rhythms, particularly in identifying outputs the clock, including RNAs, proteins, and metabolites, whose abundance oscillates throughout day. These methods hold significant promise for future discovery, when combined with computational modeling. However, genome-scale experiments are costly laborious, yielding “big data” that conceptually statistically difficult analyze. There is no obvious consensus regarding design or analysis. Here we discuss relevant technical considerations generate reproducible, sound, broadly useful data. Rather than suggest a set rigid rules, aim codify principles by which investigators, reviewers, readers primary literature can evaluate suitability different experimental designs measuring aspects rhythms. We introduce CircaInSilico, web-based application generating synthetic genome data benchmark statistical studying Finally, several unmet analytical needs, applications clinical medicine, productive avenues address them.

Language: Английский

Citations

252
A Conserved Bicycle Model for Circadian Clock Control of Membrane Excitability DOI Creative Commons
Matthieu Flourakis,

Elżbieta Kula-Eversole,

Alan L. Hutchison

et al.

Cell, Journal Year: 2015, Volume and Issue: 162(4), P. 836 - 848

Published: Aug. 1, 2015

Language: Английский

Citations

209
Circadian rhythms in the absence of the clock gene Bmal1 DOI Open Access
Sandipan Ray, Utham K. Valekunja, Alessandra Stangherlin

et al.

Science, Journal Year: 2020, Volume and Issue: 367(6479), P. 800 - 806

Published: Feb. 14, 2020

Circadian (~24 hour) clocks have a fundamental role in regulating daily physiology. The transcription factor BMAL1 is principal driver of molecular clock mammals. Bmal1 deletion abolishes 24-hour activity patterning, one measure output. We determined whether function necessary for oscillations skin fibroblasts and liver slices. Unexpectedly, knockout mice, both tissues exhibited the transcriptome, proteome, phosphoproteome over 2 to 3 days absence any exogenous drivers such as light or temperature cycles. This demonstrates competent pacemaker knockouts. suggest that might be underpinned by transcriptional regulation recruitment ETS family factors, nontranscriptionally co-opting redox oscillations.

Language: Английский

Citations

194
NAD+ Controls Circadian Reprogramming through PER2 Nuclear Translocation to Counter Aging DOI Creative Commons
Daniel C. Levine,

Hee‐Kyung Hong,

Benjamin J. Weidemann

et al.

Molecular Cell, Journal Year: 2020, Volume and Issue: 78(5), P. 835 - 849.e7

Published: May 4, 2020

Language: Английский

Citations

148
A photoregulatory mechanism of the circadian clock in Arabidopsis DOI
Xu Wang, Bochen Jiang, Lianfeng Gu

et al.

Nature Plants, Journal Year: 2021, Volume and Issue: 7(10), P. 1397 - 1408

Published: Oct. 14, 2021

Language: Английский

Citations

128
Repression of latent NF-κB enhancers by PDX1 regulates β cell functional heterogeneity DOI Creative Commons
Benjamin J. Weidemann, Biliana Marcheva, Mikoto Kobayashi

et al.

Cell Metabolism, Journal Year: 2024, Volume and Issue: 36(1), P. 90 - 102.e7

Published: Jan. 1, 2024

Interactions between lineage-determining and activity-dependent transcription factors determine single-cell identity function within multicellular tissues through incompletely known mechanisms. By assembling a atlas of chromatin state human islets, we identified β cell subtypes governed by either high or low activity the factor pancreatic duodenal homeobox-1 (PDX1). cells with reduced PDX1 displayed increased accessibility at latent nuclear κB (NF-κB) enhancers. Pdx1 hypomorphic mice exhibited de-repression NF-κB impaired glucose tolerance night. Three-dimensional analyses in tandem immunoprecipitation (ChIP) sequencing revealed that silences circadian inflammatory enhancers long-range contacts involving SIN3A. Conversely, Bmal1 ablation disrupted genome-wide DNA binding. Finally, antagonizing interleukin (IL)-1β receptor, an target, improved insulin secretion islets. Our studies reveal functional single defined gradient identify as target for insulinotropic therapy.

Language: Английский

Citations

17
Universal method for robust detection of circadian state from gene expression DOI Creative Commons
Rosemary Braun, William L. Kath, Marta Iwanaszko

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2018, Volume and Issue: 115(39)

Published: Sept. 10, 2018

Circadian clocks play a key role in regulating vast array of biological processes, with significant implications for human health. Accurate assessment physiological time using transcriptional biomarkers found blood can significantly improve diagnosis circadian disorders and optimize the delivery therapeutic treatments. To be useful, such test must accurate, minimally burdensome to patient, readily generalizable new data. A major obstacle development gene expression biomarker tests is diversity measurement platforms inherent variability data, often resulting predictors that perform well original datasets but cannot universally applied samples collected other settings. Here, we introduce TimeSignature, an algorithm robustly infers from expression. We demonstrate its application data three independent studies distinct microarrays further validate it against set profiled by RNA-sequencing. Our results show TimeSignature more accurate efficient than competing methods, estimating within 2 h majority samples. Importantly, once trained on single study, predictor yield highly differences study population, patient protocol, or assay platform without renormalizing retraining. This feature unique among expression-based addresses challenge generalizable, clinically useful tests.

Language: Английский

Citations

149
Circadian deep sequencing reveals stress-response genes that adopt robust rhythmic expression during aging DOI Creative Commons
Rachael Kuintzle,

Eileen S. Chow,

Tara N. Westby

et al.

Nature Communications, Journal Year: 2017, Volume and Issue: 8(1)

Published: Feb. 21, 2017

Abstract Disruption of the circadian clock, which directs rhythmic expression numerous output genes, accelerates aging. To enquire how system protects aging organisms, here we compare transcriptomes in heads young and old Drosophila melanogaster . The core clock most genes remained robustly flies, while others lost rhythmicity with age, resulting constitutive over- or under-expression. Unexpectedly, identify a subset that adopted increased de novo during aging, enriched for stress-response functions. These termed late-life cyclers, were also rhythmically induced flies by constant exposure to exogenous oxidative stress, this upregulation is CLOCK-dependent. We age-onset several putative primary piRNA transcripts overlapping antisense transposons. Our results suggest that, as organisms shifts greater regulatory priority mitigation accumulating cellular stress.

Language: Английский

Citations

108