Genome-wide profiling of circular RNAs,alternative splicing,and R-loops in stem-differentiating xylem of Populus trichocarpa  

作　　者：Xuqing Liu Yubang Gao Jiakai Liao Miao Miao Kai Chen Feihu Xi Wentao Wei Huihui Wang Yongsheng Wang XiXu Anireddy S.N.Reddy Lianfeng Gu 

机构地区：[1]Basic Forestry and Proteomics Research Center,College of Forestry,Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology,Fujian Agriculture and Forestry University,Fuzhou 350002,China [2]Basic Forestry and Proteomics Research Center,College of Life Science,Fujian Agriculture and Forestry University,Fuzhou 350002,China [3]Department of Biology and Program in Cell and Molecular Biology,Colorado State University,Fort Collins,Colorado 80523,USA

出　　处：《Journal of Integrative Plant Biology》2021年第7期1294-1308,共15页植物学报（英文版）

基　　金：supported by the National Key R&D Programof China(2016YFD0600106).

摘　　要：Circular RNAs(circRNAs)are a recently dis-covered type of non‐coding RNA derived from pre‐mRNAs.R‐loops consist of a DNA:RNA hybrid andthe associated single‐stranded DNA.InArabi-dopsis thaliana,circRNA:DNA R‐loops regulatealternative splicing(AS)ofSEPALLATA3(SEP3).However,the occurrence and functions ofcircRNAs and R‐loops inPopulus trichocarpaarelargely unexplored.Here,we performed circRNA‐enriched sequencing in the stem‐differentiatingxylem(SDX)ofP.trichocarpaand identified 2,742distinct circRNAs,including circ‐CESA4,circ‐IRX7,and circ‐GUX1,which are generated from genesinvolved in cellulose,and hemicellulose biosyn-thesis,respectively.To investigate the roles ofcircRNAs in modulating alternative splicing(AS),we detected 7,836 AS events using PacBio Iso‐Seq and identified 634 circRNAs that overlappedwith 699 AS events.Furthermore,using DNA:RNAhybrid immunoprecipitation followed by se-quencing(DRIP‐seq),we identified 8,932 R‐looppeaks that overlapped with 181 circRNAs and 672AS events.Notably,several SDX‐related circRNAsoverlapped with R‐loop peaks,pointing to theirpossible roles in modulating AS in SDX.Indeed,overexpressing circ‐IRX7increased the levels ofR‐loop structures and decreased the frequency ofintron retention in linearIRX7transcripts.Thisstudy provides a valuable R‐loop atlas resourceand uncovers the interplay between circRNAs andAS in SDX ofP.trichocarpa.

关 键 词：alternative splicing circular RNA R‐loop Populustrichocarpa stem‐differentiating xylem 

分 类 号：S792.11[农业科学—林木遗传育种]