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Genome‐wide profiling of circular RNAs, alternative splicing, and R‐loops in stem‐differentiating xylem of Populus trichocarpa
Author(s) -
Liu Xuqing,
Gao Yubang,
Liao Jiakai,
Miao Miao,
Chen Kai,
Xi Feihu,
Wei Wentao,
Wang Huihui,
Wang Yongsheng,
Xu Xi,
Reddy Anireddy S.N.,
Gu Lianfeng
Publication year - 2021
Publication title -
journal of integrative plant biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.734
H-Index - 83
eISSN - 1744-7909
pISSN - 1672-9072
DOI - 10.1111/jipb.13081
Subject(s) - populus trichocarpa , biology , intron , rna , rna splicing , gene , xylem , arabidopsis , computational biology , genetics , genome , botany , mutant
Circular RNAs (circRNAs) are a recently discovered type of non‐coding RNA derived from pre‐mRNAs. R‐loops consist of a DNA:RNA hybrid and the associated single‐stranded DNA. In Arabidopsis 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 biosynthesis, 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 sequencing (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 .