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Genome-wide profiling of circular RNAs, alternative splicing, and R-loops in stem-differentiating xylem of Populus trichocarpa. 2021

Xuqing Liu, and Yubang Gao, and Jiakai Liao, and Miao Miao, and Kai Chen, and Feihu Xi, and Wentao Wei, and Huihui Wang, and Yongsheng Wang, and Xi Xu, and Anireddy S N Reddy, and Lianfeng Gu
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.

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.

UI MeSH Term Description Entries
D002454 Cell Differentiation Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs. Differentiation, Cell,Cell Differentiations,Differentiations, Cell
D000079962 RNA, Circular RNA molecules in which the 3' and 5' ends are covalently joined to form a closed continuous loop. They are resistant to digestion by EXORIBONUCLEASES. Circular Intronic RNA,Circular RNA,Circular RNAs,Closed Circular RNA,ciRNA,circRNA,circRNAs,Circular RNA, Closed,Intronic RNA, Circular,RNA, Circular Intronic,RNA, Closed Circular,RNAs, Circular
D000080870 R-Loop Structures An RNA-DNA hybrid structure formed when newly transcribed RNA remains bound to its DNA template. Stability of R-loops may play a role in GENETIC INSTABILITY. R-Loop,R-Loops,R Loop,R Loop Structures,R Loops,R-Loop Structure
D017398 Alternative Splicing A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different. RNA Splicing, Alternative,Splicing, Alternative,Alternate Splicing,Nested Transcripts,Alternate Splicings,Alternative RNA Splicing,Alternative RNA Splicings,Alternative Splicings,Nested Transcript,RNA Splicings, Alternative,Splicing, Alternate,Splicing, Alternative RNA,Splicings, Alternate,Splicings, Alternative,Splicings, Alternative RNA,Transcript, Nested,Transcripts, Nested
D052584 Xylem Plant tissue that carries water up the root and stem. Xylem cell walls derive most of their strength from LIGNIN. The vessels are similar to PHLOEM sieve tubes but lack companion cells and do not have perforated sides and pores. Xylems
D032107 Populus A plant genus of the family SALICACEAE. Balm of Gilead is a common name used for P. candicans, or P. gileadensis, or P. jackii, and sometimes also used for ABIES BALSAMEA or for COMMIPHORA. Cottonwood,Poplar, Balsam,Poplar, Black,Poplar, True,Populus balsamifera,Populus fremontii,Populus nigra,Balsam Poplar,Balsam Poplars,Black Poplar,Black Poplars,Cottonwoods,Poplars, Balsam,Poplars, Black,Poplars, True,Populus balsamiferas,Populus fremontius,Populus nigras,True Poplar,True Poplars,balsamiferas, Populus,fremontius, Populus,nigras, Populus

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