Multi-exponential DNA Residence Behaviors of Transcription Factors Under The Discrete Affinity Model DOI Creative Commons
Zafer Koşar, Aykut Erbaş

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Сен. 23, 2023

The transcription process is regulated by temporal interactions of factors with DNA. In the last decade, computational and experimental studies revealed residence times on DNA correlate transcriptional output. Biochemical suggest that factor bindings exhibit bi-exponential dynamics, often explained binary affinity model composed nonspecific specific protein-DNA interactions. Recently, were shown to display a power law in vivo implicating effective controlling dissociation kinetics are rather more complex than suggested. One contribution can cause such continuous residence-time distributions could be higher-order complexes or protein coacervates. Here, using molecular dynamics simulations coarse-grained polymer for bacterial chromosomes interacting homodimeric at physiologically relevant concentrations, we demonstrate time dimeric proteins follow multi-exponential pattern even when single interaction describes between protein. Our reveal this emergent behavior due formation DNA-protein clusters various sizes wide range concentrations affinities. These findings add another layer regulation and, consequently, gene expression connecting affinities, clusters, factors.

Язык: Английский

Native Australian seedlings exhibit novel strategies to acclimate to repeated heatwave events DOI Creative Commons
Philippa R. Alvarez, Rosalie J. Harris, Alicia M. Cook

и другие.

Oecologia, Год журнала: 2025, Номер 207(6)

Опубликована: Май 15, 2025

Язык: Английский

Процитировано

0
Analysis of Transcriptional and Metabolic Differences in the Petal Color Change Response to High-Temperature Stress in Various Chrysanthemum Genotypes DOI Creative Commons
Zhimei Li, Zhou Hou-gao, Ying Chen

и другие.

Agronomy, Год журнала: 2024, Номер 14(12), С. 2863 - 2863

Опубликована: Ноя. 30, 2024

Flower color is one of the most important ornamental traits chrysanthemums. Previous studies have shown that high temperatures can cause petals some chrysanthemum varieties to fade; however, molecular mechanisms behind this phenomenon remain poorly understood. This study examines change in purple chrysanthemums under high-temperature stress using combined metabolomic and transcriptomic analyses. Four varieties—two heat-stable (‘Zi Feng Che’ ‘Chrystal Regal’) two heat-sensitive Hong Tuo Gui’ ‘Zi Lian’)—were analyzed. High-temperature conditions (35 °C) significantly downregulated key anthocyanins varieties, particularly cyanidin-3-O-(3″,6″-O-dimalonyl)glucoside pelargonidin-3-O-(3″,6″-O-dimalonyl)glucoside. Transcriptome analysis revealed differential gene expression involved anthocyanin biosynthesis degradation, with significant enrichment MAPK signaling, phenylpropanoid biosynthesis, flavonoid pathways. The highlighted CHS, DFR, ANS, GT1, 3AT, UGT75C1 genes synthesis between heat-tolerant varieties. Compared exhibited greater heat-responsive transcription factors, including HSFs, ERFs, MYBs, WRKYs. Genes show a negative correlation anthocyanins, Cse_sc012959.1_g030.1 (βG), Cse_sc001798.1_g020.1 (MYB), Cse_sc006944.1_g010.1 Cse_sc000572.1_g090.1 (HSF), might regulate accumulation response stress. These results provide guidance for cultivation management variety selection conditions. Additionally, they lay foundation elucidating flower stability heat breeding new

Язык: Английский

Процитировано

3
Thermosensing and thermal responses in plants DOI
Junwen Wu, Peng Liu, Yukun Liu

и другие.

Trends in Biochemical Sciences, Год журнала: 2023, Номер 48(11), С. 923 - 926

Опубликована: Авг. 30, 2023

Язык: Английский

Процитировано

7
Impact of heat and cold shock on epigenetics and chromatin structure DOI Creative Commons
Claudio Casali,

Luca Galgano,

Lorena Zannino

и другие.

European Journal of Cell Biology, Год журнала: 2023, Номер 103(1), С. 151373 - 151373

Опубликована: Ноя. 23, 2023

Cells are continuously exposed to various sources of insults, among which temperature variations extremely common. Epigenetic mechanisms, critical players in gene expression regulation, undergo alterations due these stressors, potentially leading health issues. Despite the significance DNA methylation and histone modifications their changes following heat cold shock human cells remain poorly understood. In this study, we investigated epigenetic profiles subjected hyperthermia hypothermia, revealing significant variations. Heat primarily led increments associated with silencing. contrast, presented a complex scenario, both demethylation levels increasing, indicating different responses opposite thermal stresses. These temperature-induced epigenome, particularly impact on chromatin structural organization, represent an understudied area that could offer important insights into genome function potential prospects for therapeutic targets.

Язык: Английский

Процитировано

7
Global climate change promotes aboveground growth and high-latitude species distribution in medicinal plants: Insights from the genus Panax DOI
Yan Qi, Xin‐Ke Zhang,

M. Li

и другие.

Journal of Cleaner Production, Год журнала: 2024, Номер unknown, С. 143863 - 143863

Опубликована: Окт. 1, 2024

Язык: Английский

Процитировано

2
Histone demethylase JMJ713 interaction with JMJ708 modulating H3K36me2, enhances rice heat tolerance through promoting hydrogen peroxide scavenging DOI

Jiaxin Chai,

Xiangyang Gu,

Pengyu Song

и другие.

Plant Physiology and Biochemistry, Год журнала: 2024, Номер 217, С. 109284 - 109284

Опубликована: Ноя. 8, 2024

Язык: Английский

Процитировано

1
Epigenetic memory of temperature sensed during somatic embryo maturation in 2-year-old maritime pine trees DOI
Jean‐François Trontin, Mamadou Dia Sow, Alain Delaunay

и другие.

PLANT PHYSIOLOGY, Год журнала: 2024, Номер unknown

Опубликована: Ноя. 7, 2024

Abstract Embryogenesis is a brief but potentially critical phase in the life cycle of tree for adaptive phenotypic plasticity. Using somatic embryogenesis maritime pine (Pinus pinaster Ait.), we found that temperature during maturation affects embryo development and postembryonic growth up to 3 yr. We examined whether this stress memory could stem from temperature- and/or development-induced changes DNA methylation. For this, developed 200 mb custom sequence capture bisulfite analysis genes promoters identify differentially methylated cytosines (DMCs) between treatments (18, 23, 28 °C) developmental stages (immature cotyledonary embryos, shoot apical meristem 2-yr-old plants) investigate if these differences can be mitotically transmitted embryonic (epigenetic memory). revealed high prevalence temperature-induced DMCs (8% 14%) compared (<1%) all cytosine contexts. Developmental showed comparable pattern only CG context with strong trend toward hypomethylation, particularly promoters. A percentage induced by transitions were memorized (up 45%–50%) 90%). By contrast, was lower confined after both 8%). stringent criteria, identified 10 involved defense responses adaptation, development, chromatin regulation are candidates establishment persistent epigenetic sensed pine. Here, provide evidence methylation marks established plant phase.

Язык: Английский

Процитировано

1
Epigenetic memory of temperature during somatic embryo maturation in 2-year-old maritime pine trees DOI
Jean‐François Trontin, Mamadou Dia Sow, Alain Delaunay

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июнь 30, 2024

Abstract Embryogenesis is a brief but potentially critical phase in the tree life cycle for adaptive phenotypic plasticity. Using somatic embryogenesis maritime pine, we found that temperature during maturation affects embryo development and post-embryonic growth up to three years. We examined whether this stress memory could stem from temperature- and/or development-induced changes DNA methylation. To do this, developed 200 Mb custom sequence capture bisulfite analysis of genes promoters identify differentially methylated cytosines (DMCs) between treatments (18, 23, 28°C) developmental stages (immature cotyledonary embryos, shoot apical meristem 2-year-old plants) investigate if these differences can be mitotically transmitted embryonic (epigenetic memory). revealed high prevalence temperature-induced DMCs (8-14%) compared (less than 1%) all 3 cytosine contexts. Developmental showed comparable pattern only CG context, with trend towards hypo-methylation, particularly promoters. A percentage induced by transitions were memorized (up 45-50%) 90%). In contrast, was lower confined after both 14%) 8%). stringent criteria, identified ten involved defense responses adaptation, chromatin regulation are candidates establishment persistent epigenetic sensed pine. Graphical abstract

Язык: Английский

Процитировано

0
Multiple Omics Analyses Reveal Activation of Nitrogen Metabolism and Flavonoid Glycosylation in Toxicodendron vernicifluum Under High Temperature DOI Creative Commons
Guoqing Bai,

Ruiwen Ding,

Qi Su

и другие.

Biology, Год журнала: 2024, Номер 13(11), С. 876 - 876

Опубликована: Окт. 28, 2024

Lacquer trees (

Язык: Английский

Процитировано

0
Native Australian seedlings exhibit novel strategies to acclimate to repeated heatwave events DOI Creative Commons
Philippa R. Alvarez, Rosalie J. Harris, Alicia M. Cook

и другие.

Research Square (Research Square), Год журнала: 2024, Номер unknown

Опубликована: Ноя. 19, 2024

Abstract 1. Heatwaves are becoming more intense and frequent. Plant photosystem thermal thresholds can vary with species, but also shift in response to environmental triggers. Both upper lower acclimate repeated heatwaves through ecological stress memory, where prior exposure primes them for subsequent events. The extent which acclimation heat events varies among origin and/or species is unknown. Different strategies might reflect biome of origin, or may be species-specific. 2. For 12 from two contrasting biomes – extreme desert benign coastal temperate we investigated responses simulated heatwaves, via shifts critical temperatures II, the difference between these thresholds, tolerance breadth (TTB). 3. Biome had no effect on tolerance. Observed differences following suggested possible acclimatory strategies. In some cases, increased during first heatwave, at cost reduced second a sprinter strategy. Other acclimated heatwave further indicative marathoner 4. Synthesis: These among-species could suggest distinct vulnerabilities resilience repeat events, having limited capacity tolerate consecutive possibly as too great, other advantage helping survive future stress, least short-term.

Язык: Английский

Процитировано

0