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), Journal Year: 2023, Volume and Issue: unknown

Published: Sept. 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.

Language: Английский

How Rice Responds to Temperature Changes and Defeats Heat Stress DOI Creative Commons
Yufeng Xing, Hongyu Lu,

Xinxing Zhu

et al.

Rice, Journal Year: 2024, Volume and Issue: 17(1)

Published: Nov. 29, 2024

With the intensification of greenhouse effect, a series natural phenomena, such as global warming, are gradually recognized; when ambient temperature increases to extent that it causes heat stress in plants, agricultural production will inevitably be affected. Therefore, several issues associated with crops urgently need solved. Rice is one momentous food for humans, widely planted tropical and subtropical monsoon regions. It prone high summer, leading decrease yield quality. Understanding how rice can tolerate through genetic effects particularly vital. This article reviews respond rising by integrating molecular regulatory pathways introduce its physiological mechanisms tolerance from perspective biology. In addition, genome selection engineering were emphasized provide theoretical basis sustainability stability crop yield-quality structures under temperatures point view breeding.

Language: Английский

Citations

3
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

et al.

Agronomy, Journal Year: 2024, Volume and Issue: 14(12), P. 2863 - 2863

Published: Nov. 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

Language: Английский

Citations

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

et al.

Trends in Biochemical Sciences, Journal Year: 2023, Volume and Issue: 48(11), P. 923 - 926

Published: Aug. 30, 2023

Language: Английский

Citations

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

Luca Galgano,

Lorena Zannino

et al.

European Journal of Cell Biology, Journal Year: 2023, Volume and Issue: 103(1), P. 151373 - 151373

Published: Nov. 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.

Language: Английский

Citations

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

et al.

Journal of Cleaner Production, Journal Year: 2024, Volume and Issue: unknown, P. 143863 - 143863

Published: Oct. 1, 2024

Language: Английский

Citations

1
Histone demethylase JMJ713 interaction with JMJ708 modulating H3K36me2, enhances rice heat tolerance through promoting hydrogen peroxide scavenging DOI

Jiaxin Chai,

Xiangyang Gu,

Pengyu Song

et al.

Plant Physiology and Biochemistry, Journal Year: 2024, Volume and Issue: 217, P. 109284 - 109284

Published: Nov. 8, 2024

Language: Английский

Citations

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

et al.

PLANT PHYSIOLOGY, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 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.

Language: Английский

Citations

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

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 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

Language: Английский

Citations

0
Epigenomic, cistromic, and transcriptomic profiling of primary kidney tubular cells DOI Open Access
Zhiheng Liu, Lirong Zhang, Yupeng Chen

et al.

Journal of Biological Methods, Journal Year: 2024, Volume and Issue: 11(2), P. e99010015 - e99010015

Published: July 10, 2024

Spatiotemporal regulation of gene expression is essential for maintaining cellular homeostasis throughout kidney development and disease progression. Transcription factors (TFs) epigenetic modifications play pivotal roles in controlling expression. Profiling chromatin across the genome, along with distribution target by TFs specific cell types, crucial understanding dynamic changes Here, we presented a comprehensive workflow epigenomic, cistromic, transcriptomic analyses primary tubular cells. Specifically, our methodologies included isolation epithelial cells, RNA extraction, assay transposase-accessible using sequencing, ultra-low-input micrococcal nuclease-based native immunoprecipitation, cleavage under targets release nuclease, subsequent bioinformatic analysis. This protocol provides methodological framework investigating diseases.

Language: Английский

Citations

0
Transcriptome analysis of maize resistance to Fusarium verticillioides DOI Creative Commons

Hui Zeng,

Hongyu Cai,

Tianhang Bai

et al.

Journal of Plant Interactions, Journal Year: 2024, Volume and Issue: 19(1)

Published: Aug. 28, 2024

Maize (Zea mays) is a crucial crop for both food and economic purposes. Fusarium verticillioides known to cause ear rot in corn, leading reduction corn yield. Understanding the regulatory network of maize resistance this identifying key genes associated with disease resistance. The study revealed that inbred line J1259 exhibited by increasing activities POD CAT enzymes. Transcriptome analysis at 48 96 hours post-infection large number DEGs involved plant-pathogen interactions, MAPK signaling pathways-plants plant hormone were significant up-regulated. Additionally, transcription factors related signaling, particularly ARF family auxin regulation, enriched. These results lay foundation further investigations into mechanisms underlying response J1259.

Language: Английский

Citations

0