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

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 and the associated single-stranded DNA. In Arabi-dopsis thaliana, circRNA:DNA R-loops regulate alternative splicing (AS) of SEPALLATA3 (SEP3). However, the occurrence and functions of circRNAs and R-loops in Populus trichocarpa are largely unexplored. Here, we performed circRNA-enriched sequencing in the stem-differentiating xylem (SDX) of P. trichocarpa and identified 2,742 distinct circRNAs, including circ-CESA4, circ-IRX7, and circ-GUX1, which are generated from genes involved in cellulose, and hemicellulose biosyn-thesis, respectively. To investigate the roles of circRNAs in modulating alternative splicing (AS), we detected 7,836 AS events using PacBio Iso-Seq and identified 634 circRNAs that overlapped with 699 AS events. Furthermore, using DNA:RNA hybrid immunoprecipitation followed by se-quencing (DRIP-seq), we identified 8,932 R-loop peaks that overlapped with 181 circRNAs and 672 AS events. Notably, several SDX-related circRNAs overlapped with R-loop peaks, pointing to their possible roles in modulating AS in SDX. Indeed, overexpressing circ-IRX7 increased the levels of R-loop structures and decreased the frequency of intron retention in linear IRX7 transcripts. This study provides a valuable R-loop atlas resource and uncovers the interplay between circRNAs and AS in SDX of P. trichocarpa.

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作者 Xuqing Liu [1] Yubang Gao [2] Jiakai Liao [2] Miao Miao [1] Kai Chen [2] Feihu Xi [2] Wentao Wei [1] Huihui Wang [1] Yongsheng Wang [2] Xi Xu [2] Anireddy S.N.Reddy [3] Lianfeng Gu [1] 学术成果认领
作者单位 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 [1] Basic Forestry and Proteomics Research Center,College of Life Science,Fujian Agriculture and Forestry University,Fuzhou 350002,China [2] Department of Biology and Program in Cell and Molecular Biology,Colorado State University,Fort Collins,Colorado 80523,USA [3]
栏目名称 Functional Omics and Systems Biology
发布时间 2021-08-02
基金项目
This work was supported by the National Key R&D Program of China
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植物学报(英文版)

植物学报(英文版)

2021年63卷7期

1294-1308页

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