Layers of crosstalk between circadian regulation and environmental signalling in plants

Current Biology, Journal Year: 2021, Volume and Issue: 31(8), P. R399 - R413

Published: April 1, 2021

Language: Английский

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Circadian regulation of the transcriptome in a complex polyploid crop

PLoS Biology, Journal Year: 2022, Volume and Issue: 20(10), P. e3001802 - e3001802

Published: Oct. 13, 2022

The circadian clock is a finely balanced timekeeping mechanism that coordinates programmes of gene expression. It currently unknown how the regulates expression homoeologous genes in polyploids. Here, we generate high-resolution time-course dataset to investigate balance between sets 3 (triads) from hexaploid bread wheat. We find large proportion triads exhibit imbalanced rhythmic patterns, with no specific subgenome favoured. In wheat, period lengths transcripts are found be longer and have higher level variance than other plant species. Expression associated controlled biological processes largely conserved wheat Arabidopsis; however, striking differences seen agriculturally critical such as starch metabolism. Together, this work highlights ongoing selection for versus diversification homoeologs identifies clock-controlled pathways might provide important targets future breeding.

Language: Английский

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Spatially specific mechanisms and functions of the plant circadian clock

PLANT PHYSIOLOGY, Journal Year: 2022, Volume and Issue: 190(2), P. 938 - 951

Published: May 28, 2022

Abstract Like many organisms, plants have evolved a genetic network, the circadian clock, to coordinate processes with day/night cycles. In plants, clock is pervasive regulator of development and modulates aspects physiology. Clock-regulated range from correct timing growth cell division interactions root microbiome. Recently developed techniques, such as single-cell time-lapse microscopy RNA-seq, are beginning revolutionize our understanding this regulation, revealing surprising degree organ, tissue, cell-type specificity. review, we highlight recent advances in spatial view across plant, both terms how it regulated regulates diversity output processes. We outline these spatially specific functions will help reveal ways that provides fitness benefit for plant.

Language: Английский

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Circadian- and Light-Driven Rhythmicity of Interconnected Gene Networks in Olive Tree

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(1), P. 361 - 361

Published: Jan. 3, 2025

A circadian clock (CC) has evolved in plants that synchronizes their growth and development with daily seasonal cycles. properly functioning contributes to increasing plant growth, reproduction, competitiveness. In plants, continuous light treatment been a successful approach for obtaining novel knowledge about the clock. The olive tree (Olea europaea L.) is one of most important crops Mediterranean area, and, so far, limited information available on its CC gene network. Here, we studied behavior rhythm genes under LD (light/darkness) LL (light/light) conditions, relationships this network, ability treatments modulate expression photoprotective pigment lipid biosynthesis pathways. One month conditions increased performance, but exposure also caused reductions vegetative chlorophyll accumulation. panel was designed study transcription levels involved perception, CC, secondary metabolite fatty acid biosynthesis. Our results revealed 78% transcripts exhibited intraday differences them retained rhythmicity after two months conditions. Furthermore, co-regulation within complex network among photoreceptors, anthocyanidins, acids orchestrated by factor HY5. This research enriches our trees grown prolonged irradiation, which may be attractive scientific community breeding programs improvement species.

Language: Английский

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Regulatory principles of photoperiod-driven clock function in plants

Trends in Plant Science, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 1, 2025

The circadian clock provides a fundamental timing mechanism for plant fitting to seasonal changes in the photoperiod. Although photoperiodic regulation of developmental transition has been studied several species, our understanding core parallelisms across species is sparse. Here we present comparative analysis networks by identifying common regulatory principles that govern key genes transition. Using time-course transcriptomic datasets from long-day plants and short-day taken different photoperiods, propose model integrates minimal set components predict necessary conditions governing species-specific outputs. This study identifies patterns associated with function plants, linking photoperiod interpretation architecture.

Language: Английский

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

New Phytologist, Journal Year: 2025, Volume and Issue: unknown

Published: March 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

Language: 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, Journal Year: 2025, Volume and Issue: 16(1)

Published: May 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 ).

Language: Английский

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Circadian coordination of cellular processes and abiotic stress responses

Current Opinion in Plant Biology, Journal Year: 2021, Volume and Issue: 64, P. 102133 - 102133

Published: Nov. 10, 2021

Diel changes in the environment are perceived by circadian clock which transmits temporal information throughout plant cell to synchronize daily and seasonal environmental signals with internal biological processes. Dynamic modulations of diverse levels gene regulation within impacted stress. Recent insights into control cellular processes such as alternative splicing, polyadenylation, noncoding RNAs discussed. We highlight studies on reactive oxygen species, calcium signaling, gating temperature stress responses. Finally, we briefly summarize recent work translation-specific rhythmicity cycle genes subcellular localization relocalization oscillator components. Together, this mini-review highlights these events context responses Arabidopsis.

Language: Английский

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Interpreting machine learning models to investigate circadian regulation and facilitate exploration of clock function

Proceedings of the National Academy of Sciences, Journal Year: 2021, Volume and Issue: 118(32)

Published: Aug. 5, 2021

Significance The circadian clock is an internal molecular 24-h timer that critical to life on Earth. We describe a series of artificial intelligence (AI)– and machine learning (ML)–based approaches enable more cost-effective analysis insight into regulation function. Throughout the manuscript, we illuminate what inside ML “black box” via explanation or interpretation predictive models. Using this our models, derive biological insights why prediction was made, alongside accurate predictions. Most innovatively, use only DNA sequence features for gene expression prediction. explainable AI, define possible, responsible regulatory elements as make these predictions; critically requires no prior knowledge elements.

Language: Английский

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Alternative Splicing in the Regulatory Circuit of Plant Temperature Response

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(4), P. 3878 - 3878

Published: Feb. 15, 2023

As sessile organisms, plants have evolved complex mechanisms to rapidly respond ever-changing ambient temperatures. Temperature response in is modulated by a multilayer regulatory network, including transcriptional and post-transcriptional regulations. Alternative splicing (AS) an essential mechanism. Extensive studies confirmed its key role plant temperature response, from adjustment diurnal seasonal changes extreme temperatures, which has been well documented previous reviews. node the AS can be various upstream regulations, such as chromatin modification, transcription rate, RNA binding proteins, structure modifications. Meanwhile, number of downstream are affected AS, nonsense-mediated mRNA decay (NMD) pathway, translation efficiency production different protein variants. In this review, we focus on links between regulation other response. Recent advances regarding how regulated following consequences gene functional modulation will discussed. Substantial evidence suggests that network integrating unveiled.

Language: Английский

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