Circadian gating: concepts, processes, and opportunities

Philosophical Transactions of the Royal Society B Biological Sciences, Год журнала: 2025, Номер 380(1918)

Опубликована: Янв. 23, 2025

Circadian clocks provide a biological measure of time that coordinates metabolism, physiology and behaviour with 24 h cycles in the environment. systems have variety characteristic properties, such as entrainment to environmental cues, self-sustaining rhythm about temperature compensation circadian rhythm. In this perspective, we discuss process gating, which refers restriction event particular times day by clock. We introduce principles processes associated gating organisms, including some mechanisms. highlight socioeconomic opportunities presented investigation using selected examples from medicine agricultural crop production illustrate its importance. This article is part Theo Murphy meeting issue ‘Circadian rhythms infection immunity’.

Язык: Английский

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GIGANTEA Is Required for Robust Circadian Rhythms in Wheat

Plant Cell & Environment, Год журнала: 2025, Номер unknown

Опубликована: Фев. 26, 2025

ABSTRACT GIGANTEA ( GI ) is a plant‐specific protein that functions in many physiological processes and signalling networks. In Arabidopsis, has central role circadian oscillators regulating the abundance of ZEITLUPE TIMING OF CAB EXPRESSION 1 proteins essential for photoperiodic regulation flowering. We have investigated how ortholgues this component Arabidopsis contribute to rhythms yield traits, including heading (flowering) wheat. find core wheat necessary maintain robust oscillations chlorophyll fluorescence oscillator transcript abundance. The predicted lack functional results later flowering both long days short controlled environment conditions. Our support extend previous work, which suggests pathways by photoperiodism regulates are not fully conserved between Understanding molecular basis important breeders looking manipulate time develop new elite, high‐yielding cultivars.

Язык: Английский

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Introgressions lead to reference bias in wheat RNA-seq analysis

BMC Biology, Год журнала: 2024, Номер 22(1)

Опубликована: Март 7, 2024

Abstract Background RNA-seq is a fundamental technique in genomics, yet reference bias, where transcripts derived from non-reference alleles are quantified less accurately, can undermine the accuracy of quantification and thus conclusions made downstream. Reference bias analysis has to be explored complex polyploid genomes despite evidence that they often mosaic wild relative introgressions, which introduce blocks highly divergent genes. Results Here we use hexaploid wheat as model polyploid, using both simulated experimental data show alignment suffers widespread largely driven by introgressed This leads underestimation gene expression incorrect assessment homoeologue balance. By incorporating models ten genome assemblies into pantranscriptome reference, present novel method reduce readily scaled capture more variation new transcriptome becomes available. Conclusions study shows presence introgressions lead analysis. Caution should exercised researchers non-sample for methods, such one presented here, considered.

Язык: Английский

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Genome-wide circadian gating of a cold temperature response in bread wheat

PLoS Genetics, Год журнала: 2023, Номер 19(9), С. e1010947 - e1010947

Опубликована: Сен. 18, 2023

Circadian rhythms coordinate the responses of organisms with their daily fluctuating environments, by establishing a temporal program gene expression. This schedules aspects metabolism, physiology, development and behaviour according to time day. regulation in plants is extremely pervasive, important because it underpins both productivity seasonal reproduction. extends control environmental through regulatory process known as circadian gating. gating whereby clock regulates response an cue, such that magnitude identical cue varies day cue. Here, we show there genome-wide cold temperatures plants. By using bread wheat experimental model, establish crucial programs expression underlie crop major socioeconomic importance. Furthermore, identify temperature are distributed unevenly across three subgenomes, which might reflect geographical origins ancestors modern wheat.

Язык: Английский

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Natural variations of wheat EARLY FLOWERING 3 highlight their contributions to local adaptation through fine-tuning of heading time

Theoretical and Applied Genetics, Год журнала: 2023, Номер 136(6)

Опубликована: Май 26, 2023

Язык: Английский

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The Regulatory Networks of the Circadian Clock Involved in Plant Adaptation and Crop Yield

Plants, Год журнала: 2023, Номер 12(9), С. 1897 - 1897

Опубликована: Май 6, 2023

Global climatic change increasingly threatens plant adaptation and crop yields. By synchronizing internal biological processes, including photosynthesis, metabolism, responses to biotic abiotic stress, with external environmental cures, such as light temperature, the circadian clock benefits yield. In this review, we focus on multiple levels of interaction between factors, summarize recent progresses how affects addition, propose potential strategies for better utilizing current knowledge biology in production future.

Язык: Английский

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Unlocking allelic variation in circadian clock genes to develop environmentally robust and productive crops

Planta, Год журнала: 2024, Номер 259(4)

Опубликована: Фев. 22, 2024

Abstract Main conclusion Molecular mechanisms of biological rhythms provide opportunities to harness functional allelic diversity in core (and trait- or stress-responsive) oscillator networks develop more climate-resilient and productive germplasm. The circadian clock senses light temperature day–night cycles drive rhythms. integrates endogenous signals exogenous stimuli coordinate diverse physiological processes. Advances high-throughput non-invasive assays, use forward- inverse-genetic approaches, powerful algorithms are allowing quantitation variation detection genes associated with dynamics. Circadian phytohormone pathways response cues have been well documented the model plant Arabidopsis . Novel facilitates adaptation range expansion, may additional opportunity tailor crops. phase period can determine environments, while robustness amplitude enhance resilience environmental changes. plants tightly controlled by multiple interlocked transcriptional–translational feedback loops involving morning ( CCA1 , LHY ), mid-day PRR9 PRR7 PRR5 evening TOC1 ELF3 ELF4 LUX ) that maintain ticking. Significant progress has made unravel functions regulate traits, via interaction phytohormones trait-responsive genes, Altered contribute hybrid vigor as shown maize, rice. Modifying transgenesis genome-editing crops better buffering capacity stresses. Models involve gene‒phytohormone‒trait interactions novel insights orchestrate modulate facilitate breeding all season

Язык: Английский

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Homoeolog expression divergence contributes to time of day changes in transcriptomic and glucosinolate responses to prolonged water limitation in Brassica napus

The Plant Journal, Год журнала: 2025, Номер 121(4)

Опубликована: Фев. 1, 2025

SUMMARY Water availability is a major determinant of crop production, and rising temperatures from climate change are leading to more extreme droughts. To combat the effects on yields, we need develop varieties that tolerant water‐limited conditions. We aimed determine how diverse types (winter/spring oilseed, tuberous, leafy) allopolyploid Brassica napus , species contains economically important rapeseed oilseed crop, respond prolonged water limitation. exposed plants an 80% reduction in assessed growth color high‐throughput phenotyping system over 4 weeks ended experiment with tissue collection for time course transcriptomic study. found overall across cultivars but varying degrees. Diel transcriptome analyses revealed significant accession‐specific changes time‐of‐day regulation photosynthesis, carbohydrate metabolism, sulfur metabolism. Interestingly, there was extensive variation which homoeologs two parental subgenomes responded limitation could be due differences regulatory regions these lines. Follow‐up experiments select confirmed maintained photosynthetic health during while slowing growth. In examined, day levels glucosinolates, sulfur‐ nitrogen ‐rich specialized metabolites, consistent diel responses. These results suggest lines adjusting their stores under conditions through distinct regulation.

Язык: Английский

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Stable and dynamic gene expression patterns over diurnal and developmental timescales in Arabidopsis thaliana

New Phytologist, Год журнала: 2025, Номер unknown

Опубликована: Март 20, 2025

Developmental processes are known to be circadian-regulated in plants. For instance, the circadian clock regulates genes involved photoperiodic flowering pathway and initiation of leaf senescence. Furthermore, signals that entrain clock, such as energy availability, vary strength over plant development. However, diel oscillations Arabidopsis transcriptome have typically been measured seedlings. We collected RNA sequencing (RNA-seq) data from leaves developmental timescales, concurrently: every 4 h d-1, on three separate days after a synchronised vegetative-to-reproductive transition. Gene expression varied more timescale than timescale, including related key sensor: sucrose nonfermenting-1-related protein kinase complex. Moreover, regulatory targets core displayed changes rhythmicity amplitude Cell-type-specific showed patterns amplitude, but not phase, Some previously identified reverse transcription quantitative polymerase chain reaction housekeeping display undesirable levels variation both timescales. identify which common most stable across In summary, we establish transcriptional regulation development, demonstrating how change

Язык: Английский

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48-Hour and 24-Hour Time-lapse Single-nucleus Transcriptomics Reveal Cell-type specific Circadian Rhythms in Arabidopsis

Nature Communications, Год журнала: 2025, Номер 16(1)

Опубликована: Май 5, 2025

Functional circadian clock is critical to the adaptation and survival of organisms. In land plants, comprehensive profiling gene expression at single-cell level largely unknown partly due challenges in obtaining precisely-timed single cells embedded within cell walls. To bridge this gap, we employ time-lapse single-nucleus RNA sequencing (snRNA-seq) on Arabidopsis seedlings collected over a 48-hour window 4-hour intervals, as well 24-hour day 2-hour yielding total 77,142 130,000 nuclei. Here, find that four clusters shoot share coherent rhythm, while around 3000 genes display cell-type specific rhythmic expression. Our analysis indicates encoding regulators oscillate multiple types, majority them are well-documented core genes, suggesting snRNA-seq data could be used identify more components oscillating cell-autonomous way. We ABF1 regulator, whose overexpression shortens period. provides resource for plant rhythmicity (hosted https://zhailab.bio.sustech.edu.cn/sc_circadian ).

Язык: Английский

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