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

文献类型： 外文期刊

第一作者： He, Zexue

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

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 （ 影响因子：9.4； 五年影响因子：10.5 ）

ISSN： 0028-646X

年卷期： 2023 年

页码：

收录情况： SCI

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
作者其他论文 更多>>

微信小程序