Co-transcriptional splicing efficiencies differ within genes and between cell types.
Co-transcriptional splicing efficiencies differ within genes and between cell types.
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DOI：
10.1261/rna.078662.120
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发表时间：
2021-05-11
期刊：
影响因子：
--
通讯作者：
Ljungman M
中科院分区：
文献类型：
--
作者：
Bedi K;Magnuson BR;Narayanan I;Paulsen M;Wilson TE;Ljungman M
前mRNA剪接由剪接体进行，涉及剪接位点识别、内含子去除和外显子连接。剪接体的组分已显示与延伸RNA聚合酶II（RNAPII）相互作用，其被认为允许剪接与转录同时发生。然而，对人类细胞中共转录剪接的调控和效率知之甚少。在这项研究中，我们使用Bru-seq和BruChase-seq来确定在六种人类细胞系中表达的17，000个内含子的共转录剪接效率。我们发现这六个细胞系中不到一半的内含子是共转录剪接的。单个内含子的剪接效率在细胞系中表现出变化，表明剪接可能以细胞类型特异性的方式进行调节。此外，内含子的剪接效率在基因内是不同的。共转录剪接的效率与基因长度、内含子位置、剪接位点强度或内含子/相邻外显子GC含量无关。然而，我们确定了与剪接效率相关的多种RNA结合蛋白（RBP）的结合信号，包括核心剪接体机制组件，如SF 3B 4，U2 AF 1和U2 AF 2，在剪接不良的内含子中显示出更高的结合信号。此外，多个RBP，如BUD 13，SND 1，显示出优先结合的外显子侧翼内含子具有高剪接效率。这里提出的新生RNA剪接模式跨越多种细胞类型增加了我们对RNA剪接复杂性的理解，其中RNA结合蛋白可能在以细胞类型和内含子特异性方式确定剪接结果中发挥重要作用。
Pre-mRNA splicing is carried out by the spliceosome and involves splice site recognition, removal of introns, and ligation of exons. Components of the spliceosome have been shown to interact with the elongating RNA polymerase II (RNAPII), which is thought to allow splicing to occur concurrently with transcription. However, little is known about the regulation and efficiency of cotranscriptional splicing in human cells. In this study, we used Bru-seq and BruChase-seq to determine the cotranscriptional splicing efficiencies of 17,000 introns expressed across six human cell lines. We found that less than half of all introns across these six cell lines were cotranscriptionally spliced. Splicing efficiencies for individual introns showed variations across cell lines, suggesting that splicing may be regulated in a cell type–specific manner. Moreover, the splicing efficiency of introns varied within genes. The efficiency of cotranscriptional splicing did not correlate with gene length, intron position, splice site strengths, or the intron/neighboring exons GC content. However, we identified binding signals from multiple RNA-binding proteins (RBPs) that correlated with splicing efficiency, including core spliceosomal machinery components—such as SF3B4, U2AF1, and U2AF2 showing higher binding signals in poorly spliced introns. In addition, multiple RBPs, such as BUD13, PUM1, and SND1, showed preferential binding in exons that flank introns with high splicing efficiencies. The nascent RNA splicing patterns presented here across multiple cell types add to our understanding of the complexity in RNA splicing, wherein RNA-binding proteins may play important roles in determining splicing outcomes in a cell type– and intron-specific manner.
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影响因子：
4.3
作者：
Corvelo A;Hallegger M;Smith CW;Eyras E
通讯作者：
Eyras E
影响因子：
10.5
作者：
Boutz PL;Bhutkar A;Sharp PA
通讯作者：
Sharp PA
影响因子：
64.5
作者：
Bhatt DM;Pandya-Jones A;Tong AJ;Barozzi I;Lissner MM;Natoli G;Black DL;Smale ST
通讯作者：
Smale ST
影响因子：
14.9
作者：
Frankish A;Diekhans M;Ferreira AM;Johnson R;Jungreis I;Loveland J;Mudge JM;Sisu C;Wright J;Armstrong J;Barnes I;Berry A;Bignell A;Carbonell Sala S;Chrast J;Cunningham F;Di Domenico T;Donaldson S;Fiddes IT;García Girón C;Gonzalez JM;Grego T;Hardy M;Hourlier T;Hunt T;Izuogu OG;Lagarde J;Martin FJ;Martínez L;Mohanan S;Muir P;Navarro FCP;Parker A;Pei B;Pozo F;Ruffier M;Schmitt BM;Stapleton E;Suner MM;Sycheva I;Uszczynska-Ratajczak B;Xu J;Yates A;Zerbino D;Zhang Y;Aken B;Choudhary JS;Gerstein M;Guigó R;Hubbard TJP;Kellis M;Paten B;Reymond A;Tress ML;Flicek P
通讯作者：
Flicek P
影响因子：
16
作者：
Chathoth, Keerthi T.;Barrass, J. David;Webb, Shaun;Beggs, Jean D.
通讯作者：
Beggs, Jean D.