数字农科院2.0

R-loops act as regulatory switches modulating transcription of COLD-responsive genes in rice

文献类型： 外文期刊

作者： He, Zexue;Li, Mengqi;Pan, Xiucai;Peng, Yulian;Shi, Yining;Han, Qi;Shi, Manli;She, Linwei;Borovskii, Gennadii;Chen, Xiaojun;Gu, Xiaofeng;Cheng, Xuejiao;Zhang, Wenli

作者机构：

关键词： COLD responses;DNase hypersensitive sites;gene transcription;lncRNAs;Oryza sativa L.;regulatory networks;R-loops

期刊名称： NEW PHYTOLOGIST

ISSN： 0028-646X

年卷期： 2023 年

页码：

收录情况： SCIE（2023版）

摘要： COLD is a major naturally occurring stress that usually causes complex symptoms and severe yield loss in crops. R-loops function in various cellular processes, including development and stress responses, in plants. However, how R-loops function in COLD responses is largely unknown in COLD susceptible crops like rice (Oryza sativa L.).We conducted DRIP-Seq along with other omics data (RNA-Seq, DNase-Seq and ChIP-Seq) in rice with or without COLD treatment.COLD treatment caused R-loop reprogramming across the genome. COLD-biased R-loops had higher GC content and novel motifs for the binding of distinct transcription factors (TFs). Moreover, R-loops can directly/indirectly modulate the transcription of a subset of COLD-responsive genes, which can be mediated by R-loop overlapping TF-centered or cis-regulatory element-related regulatory networks and lncRNAs, accounting for c. 60% of COLD-induced expression of differential genes in rice, which is different from the findings in Arabidopsis. We validated two R-loop loci with contrasting (negative/positive) roles in the regulation of two individual COLD-responsive gene expression, as potential targets for enhanced COLD resistance.Our study provides detailed evidence showing functions of R-loop reprogramming during COLD responses and provides some potential R-loop loci for genetic and epigenetic manipulation toward breeding of rice varieties with enhanced COLD tolerance.

分类号：

  • 相关文献

[1]脂肪相关lncRNAs在动物中的研究进展. 刘怡冰,敖红,邢凯,王楚端. 2019

[2]Expression Profiles and Characteristics of Apple lncRNAs in Roots, Phloem, Leaves, Flowers, and Fruit. Wang, Dajiang,Gao, Yuan,Sun, Simiao,Li, Lianwen,Wang, Kun. 2022

[3]Dual roles of R-loops in the formation and processing of programmed DNA double-strand breaks during meiosis. Chao Liu,Wei Xu,Liying Wang,Zhuo Yang,Kuan Li,Jun Hu,Yinghong Chen,Ruidan Zhang,Sai Xiao,Wenwen Liu,Huafang Wei,Jia Yu Chen,Qianwen Sun,Wei Li. 2023

[4]Analysis and cloning of the synthetic pathway of the phytohormone indole-3-acetic acid in the plant-beneficial Bacillus amyloliquefaciens SQR9. Shao, Jiahui,Li, Shuqing,Zhang, Guishan,Zhang, Ruifu,Shao, Jiahui,Li, Shuqing,Zhang, Nan,Cui, Xiaoshuang,Zhou, Xuan,Shen, Qirong,Zhang, Ruifu,Shao, Jiahui,Li, Shuqing,Zhang, Nan,Cui, Xiaoshuang,Zhou, Xuan,Shen, Qirong,Zhang, Ruifu. 2015

[5]OsGRF4AA compromises heat tolerance of developing pollen grains in rice. Yujian Mo,Guangyan Li,Li Liu,Yingjie Zhang,Junyi Li,Meizhen Yang,Shanlan Chen,Qiaoling Lin,Guanfu Fu,Dianfeng Zheng,Yu Ling. 2023

[6]Stacking potato NLR genes activates a calcium-dependent protein kinase and confers broad-spectrum disease resistance to late blight. Zhao, Xiaoqiang,Zhang, Fan,Chen, Xiaoqing,Zhang, Chongyuan,Zhang, Haoyi,Wang, Tian,Zhang, Jinzhe,He, Cheng,Wang, Shuo,Zhang, Xinjie,Meng, Xi,Nekrasov, Vladimir,Kong, Liang,Dong, Suomeng. 2025

[7]Integrated Analysis of Long Non-Coding RNA and mRNA to Reveal Putative Candidate Genes Associated with Backfat Quality in Beijing Black Pig. Xin Liu,Weilong Tian,Ligang Wang,Longchao Zhang,Jing Liang,Lixian Wang. 2022

[8]Identification of long noncoding RNAs involved in plumule-vernalization of Chinese cabbage. Yun Dai,Guoliang Li,Xinyu Gao,Shaoxing Wang,Ze Li,Chao Song,Shifan Zhang,Fei Li,Zhiyuan Fang,Rifei Sun,Hui Zhang,Shujiang Zhang. 2023

[9]Identification of Photoperiod-Induced LncRNAs and mRNAs in Pituitary Pars Tuberalis of Sheep. Qing Xia,Mingxing Chu,Xiaoyun He,Xiaosheng Zhang,Jinlong Zhang,Xiaofei Guo,Ran Di. 2021

[10]Fat Metabolism-related lncRNA and Target Regulation and Application Studies in Chickens. Wenhao Xing,Shijie Li. 2023

[11]Pineal gland transcriptomic profiling reveals the differential regulation of lncRNA and mRNA related to prolificacy in STH sheep with two FecB genotypes. Chunyan Li,Xiaoyun He,Zijun Zhang,Chunhuan Ren,Mingxing Chu. 2021

[12]Identification And Characterization Of Mrnas A.nd Lncrnas In The U terus Of Polytocous And Monotocous Small Tail Han Sheep (Ovis Aries). La, YF, Tang, JS, He, XY, Di, R, Wang, XY, Liu, QY, Zhang, LP, Zhang, XS, Zhang, JL, Hu, WP, Chu, MX. 2019

[13]Exploring The Roles Of Fecundity-Related Long Non-Coding Rnas And Mrnas In The Adrenal Glands Of Small-Tailed Han Sheep. Xia, Q, Li, QL, Gan, SQ, Guo, XF, Zhang, XS, Zhang, JL, Chu, MX. 2020

[14]Comprehensive analysis of lncRNAs involved in skeletal muscle development in ZBED6-knockout Bama pigs. Dandan Wang,Yabin Pu,Yefang Li,Dengke Pan,Shengnan Wang,Wenjie Tian,Yuehui Ma,Lin Jiang. 2021

[15]Thyroid Transcriptomic Profiling Reveals the Follicular Phase Differential Regulation of lncRNA and mRNA Related to Prolificacy in Small Tail Han Sheep with Two FecB Genotypes. Cheng Chang,Xiaoyun He,Ran Di,Xiangyu Wang,Miaoceng Han,Chen Liang,Mingxing Chu. 2022

[16]Transcriptomic Changes of Photoperiodic Response in the Hypothalamus Were Identified in Ovariectomized and Estradiol-Treated Sheep. Xiaoyun He,Ran Di,Xiaofei Guo,Xiaohan Cao,Mei Zhou,Xiaoyu Li,Qing Xia,Xiangyu Wang,Jinlong Zhang,Xiaosheng Zhang,Qiuyue Liu,Mingxing Chu. 2022

[17]A newly identified lncRNA lnc000100 regulates proliferation and differentiation of cattle skeletal muscle cells. Mengke Ma,Mengjie Chen,Xiaoyun Wu,Suren R. Sooranna,Qingyou Liu,Deshun Shi,Jian Wang,Hui Li. 2023

[18]Key mRNAs and lncRNAs of pituitary that affect the reproduction of FecB + + small tail han sheep. Jianqi Yang,Jishun Tang,Xiaoyun He,Ran Di,Xiaosheng Zhang,Jinlong Zhang,Xiaofei Guo,Wenping Hu,Mingxing Chu. 2024

[19]Transcriptomics-based investigation of resistance differences to swine fever between large white pigs and min pigs. Jia Li,Deming Ren,Xiangxu Meng,Yiyun He,Lixian Wang,Xihui Sheng,Ligang Wang. 2025

[20]Comprehensive expression genome-wide association study of long non-coding RNAs in four porcine tissues. Liyan Deng,Marta Gòdia,Martijn F.L. Derks,Barbara Harlizius,Samin Farhangi,Zhonglin Tang,Martien A.M. Groenen,Ole Madsen. 2025

作者其他论文 更多>>