文献类型： 外文期刊

作者： He, Zexue ¹ ; Li, Mengqi ¹ ; Pan, Xiucai ¹ ; Peng, Yulian ¹ ; Shi, Yining ¹ ; Han, Qi ¹ ; Shi, Manli ¹ ; She, Linwei ¹ ; Borovskii, Gennadii ³ ; Chen, Xiaojun ⁴ ; Gu, Xiaofeng ⁵ ; Cheng, Xuejiao ¹ ; Zhang, Wenli ¹ ;

作者机构： 1.Nanjing Agr Univ, Collaborat Innovat Ctr Modern Crop Prod Cosponsore, State Key Lab Crop Genet & Germplasm Enhancement &, 1 Weigang, Nanjing 210095, Jiangsu, Peoples R China

2.Xiangyang Acad Agr Sci, Xiangyang 441057, Hubei, Peoples R China

3.Russian Acad Sci SB RAS Irkutsk, Siberian Inst Plant Physiol & Biochem, Siberian Branch, Lermontova 664033, Russia

4.Ningxia Acad Agr & Forestry Sci, Key Lab Agr Biotechnol Ningxia, Yinchuan 750002, Peoples R China

5.Chinese Acad Agr Sci, Biotechnol Res Inst, Beijing 100081, Peoples R China

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.