Circular RNAs （circRNAs） from back-splicing of exon（s） have been recently identified to be broadly expressed in eukaryotes, in tissue-and species-specific manners. Although functions of most circRNAs remain elusiv...Circular RNAs （circRNAs） from back-splicing of exon（s） have been recently identified to be broadly expressed in eukaryotes, in tissue-and species-specific manners. Although functions of most circRNAs remain elusive, some circRNAs are shown to be functional in gene expression regulation and potentially relate to diseases. Due to their stability, circRNAs can also be used as biomarkers for diagnosis. Profiling circRNAs by integrating their expression among different samples thus provides molecular basis for further functional study of circRNAs and their potential application in clinic. Here, we report CIRCpedia v2, an updated database for comprehensive circRNA annotation from over 180 RNA-seq datasets across six different species. This atlas allows users to search, browse, and download circRNAs with expression features in various cell types/tissues, including disease samples. In addition, the updated database incorporates conservation analysis of circRNAs between humans and mice. Finally, the web interface also contains computational tools to compare circRNA expression among samples. CIRCpedia v2 is accessible at http：//www.picb.ac.cn/rnomics/circpedia.展开更多
Sequences of circular RNAs(circ RNAs)produced from back-splicing of exon(s)completely overlap with those from cognate linear RNAs transcribed from the same gene loci with the exception of their back-splicing junction(...Sequences of circular RNAs(circ RNAs)produced from back-splicing of exon(s)completely overlap with those from cognate linear RNAs transcribed from the same gene loci with the exception of their back-splicing junction(BSJ)sites.Therefore,examination of global circ RNA expression from RNA-seq datasets generally relies on the detection of RNA-seq fragments spanning BSJ sites,which is different from the quantification of linear RNA expression by normalized RNA-seq fragments mapped to whole gene bodies.Thus,direct comparison of circular and linear RNA expression from the same gene loci in a genome-wide manner has remained challenging.Here,we update the previously-reported CIRCexplorer pipeline to version 3 for circular and linear RNA expression analysis from ribosomal-RNA depleted RNA-seq(CIRCexplorer3-CLEAR).A new quantitation parameter,fragments per billion mapped bases(FPB),is applied to evaluate circular and linear RNA expression individually by fragments mapped to circ RNA-specific BSJ sites or to linear RNA-specific splicing junction(SJ)sites.Comparison of circular and linear RNA expression levels is directly achieved by dividing FPBcircby FPBlinearto generate a CIRCscore,which indicates the relative circ RNA expression level using linear RNA expression level as the background.Highlyexpressed circ RNAs with low cognate linear RNA expression background can be readily identified by CIRCexplorer3-CLEAR for further investigation.CIRCexplorer3-CLEAR is publically available at https://github.com/Yang Lab/CLEAR.展开更多
Circular RNAs(circRNAs)are involved in various biological processes and disease pathogenesis.However,only a small number of functional circRNAs have been identified among hundreds of thousands of circRNA species,partl...Circular RNAs(circRNAs)are involved in various biological processes and disease pathogenesis.However,only a small number of functional circRNAs have been identified among hundreds of thousands of circRNA species,partly because most current methods are based on circular junction counts and overlook the fact that a circRNA is formed from the host gene by backsplicing(BS).To distinguish the expression difference originating from BS or the host gene,we present differentially expressed back-splicing(DEBKS),a software program to streamline the discovery of differential BS events between two rRNA-depleted RNA sequencing(RNA-seq)sample groups.By applying to real and simulated data and employing RT-qPCR for validation,we demonstrate that DEBKS is efficient and accurate in detecting circRNAs with differential BS events between paired and unpaired sample groups.DEBKS is available at https://github.com/yangence/DEBKS as open-source software.展开更多
Background： Circular RNAs （circRNAs） from back-spliced exon（s） are characterized by the covalently closed loop feature with neither 5＇ to 3＇ polarity nor polyadenylated tail. By using specific computational app...Background： Circular RNAs （circRNAs） from back-spliced exon（s） are characterized by the covalently closed loop feature with neither 5＇ to 3＇ polarity nor polyadenylated tail. By using specific computational approaches that identify reads mapped to back-splice junctions with a reversed genomic orientation, ten thousands of cireRNAs have been recently re-identified in various cell lines/tissues and across different species. Increasing lines of evidence suggest that back-splicing is catalyzed by the canonical spliceosomal machinery and modulated by cis-elements and trans-factors. Results： In this mini-review, we discuss our current understanding of circRNA biogenesis regulation, mainly focusing on the complex regulation of complementary sequences, especially Alus in human, on circRNA formation. Conclusions： Back-splicing can be significantly facilitated by RNA pair formed by orientation-opposite complementary sequences that juxtapose flanking introns of circularized exon（s）. RNA pair formed within individual introns competes with RNA pair formed across flanking introns in the same gene locus, leading to distinct choices for either canonical splicing or back-splicing. Multiple RNA pairs that bracket different circle-forming exons compete for alternative back-splicing selection, resulting in multiple circRNAs generated in a single gene locus.展开更多
基金supported by the National Natural Science Foundation of China (Grant Nos. 31730111, 31471241, and 91540115)
文摘Circular RNAs （circRNAs） from back-splicing of exon（s） have been recently identified to be broadly expressed in eukaryotes, in tissue-and species-specific manners. Although functions of most circRNAs remain elusive, some circRNAs are shown to be functional in gene expression regulation and potentially relate to diseases. Due to their stability, circRNAs can also be used as biomarkers for diagnosis. Profiling circRNAs by integrating their expression among different samples thus provides molecular basis for further functional study of circRNAs and their potential application in clinic. Here, we report CIRCpedia v2, an updated database for comprehensive circRNA annotation from over 180 RNA-seq datasets across six different species. This atlas allows users to search, browse, and download circRNAs with expression features in various cell types/tissues, including disease samples. In addition, the updated database incorporates conservation analysis of circRNAs between humans and mice. Finally, the web interface also contains computational tools to compare circRNA expression among samples. CIRCpedia v2 is accessible at http：//www.picb.ac.cn/rnomics/circpedia.
基金the Strategic Priority Research Program of Chinese Academy of Sciences,China(Grant No.XDB19020104)the National Natural Science Foundation of China(Grant Nos.31730111,31925011,and 91940306)the Howard Hughes Medical Institute International Program,the United States(Grant No.55008728).
文摘Sequences of circular RNAs(circ RNAs)produced from back-splicing of exon(s)completely overlap with those from cognate linear RNAs transcribed from the same gene loci with the exception of their back-splicing junction(BSJ)sites.Therefore,examination of global circ RNA expression from RNA-seq datasets generally relies on the detection of RNA-seq fragments spanning BSJ sites,which is different from the quantification of linear RNA expression by normalized RNA-seq fragments mapped to whole gene bodies.Thus,direct comparison of circular and linear RNA expression from the same gene loci in a genome-wide manner has remained challenging.Here,we update the previously-reported CIRCexplorer pipeline to version 3 for circular and linear RNA expression analysis from ribosomal-RNA depleted RNA-seq(CIRCexplorer3-CLEAR).A new quantitation parameter,fragments per billion mapped bases(FPB),is applied to evaluate circular and linear RNA expression individually by fragments mapped to circ RNA-specific BSJ sites or to linear RNA-specific splicing junction(SJ)sites.Comparison of circular and linear RNA expression levels is directly achieved by dividing FPBcircby FPBlinearto generate a CIRCscore,which indicates the relative circ RNA expression level using linear RNA expression level as the background.Highlyexpressed circ RNAs with low cognate linear RNA expression background can be readily identified by CIRCexplorer3-CLEAR for further investigation.CIRCexplorer3-CLEAR is publically available at https://github.com/Yang Lab/CLEAR.
基金supported by the Beijing Municipal Science and Technology Commission,China(Grant No.Z181100001518005)the Chinese Institute for Brain Research,Beijing,China to EY,the National Natural Science Foundation of China(Grant No.81873769)to CCthe Innovation Fund for Outstanding Doctoral Candidates of Peking University Health Science Center,China(Grant No.BMU2020BSS001)to ZL.
文摘Circular RNAs(circRNAs)are involved in various biological processes and disease pathogenesis.However,only a small number of functional circRNAs have been identified among hundreds of thousands of circRNA species,partly because most current methods are based on circular junction counts and overlook the fact that a circRNA is formed from the host gene by backsplicing(BS).To distinguish the expression difference originating from BS or the host gene,we present differentially expressed back-splicing(DEBKS),a software program to streamline the discovery of differential BS events between two rRNA-depleted RNA sequencing(RNA-seq)sample groups.By applying to real and simulated data and employing RT-qPCR for validation,we demonstrate that DEBKS is efficient and accurate in detecting circRNAs with differential BS events between paired and unpaired sample groups.DEBKS is available at https://github.com/yangence/DEBKS as open-source software.
文摘Background： Circular RNAs （circRNAs） from back-spliced exon（s） are characterized by the covalently closed loop feature with neither 5＇ to 3＇ polarity nor polyadenylated tail. By using specific computational approaches that identify reads mapped to back-splice junctions with a reversed genomic orientation, ten thousands of cireRNAs have been recently re-identified in various cell lines/tissues and across different species. Increasing lines of evidence suggest that back-splicing is catalyzed by the canonical spliceosomal machinery and modulated by cis-elements and trans-factors. Results： In this mini-review, we discuss our current understanding of circRNA biogenesis regulation, mainly focusing on the complex regulation of complementary sequences, especially Alus in human, on circRNA formation. Conclusions： Back-splicing can be significantly facilitated by RNA pair formed by orientation-opposite complementary sequences that juxtapose flanking introns of circularized exon（s）. RNA pair formed within individual introns competes with RNA pair formed across flanking introns in the same gene locus, leading to distinct choices for either canonical splicing or back-splicing. Multiple RNA pairs that bracket different circle-forming exons compete for alternative back-splicing selection, resulting in multiple circRNAs generated in a single gene locus.
