Conserved long-range base pairings are associated with pre-mRNA processing of human genes.
Conserved long-range base pairings are associated with pre-mRNA processing of human genes.
复制标题
DOI：
10.1038/s41467-021-22549-7
复制
发表时间：
2021-04-16
影响因子：
16.6
通讯作者：
Pervouchine D
中科院分区：
文献类型：
--
作者：
Kalmykova S;Kalinina M;Denisov S;Mironov A;Skvortsov D;Guigó R;Pervouchine D
核酸形成双链结构的能力对地球上所有生命系统都是必不可少的。目前关于RNA功能结构的知识主要集中在局部碱基对上。然而，交联和邻位连接实验表明，长距离RNA结构是高度丰富的。在这里，我们提出了最完整的人类蛋白质编码基因的保守互补区（PCCR）的目录。PCCR往往发生在内含子内，抑制插入外显子，并阻碍隐蔽和无活性剪接位点。PCCR的双链结构由降低的icSHAPE核苷酸可及性、高丰度的RNA编辑位点和频繁出现的分叉eCLIP峰支持。具有PCCR的内含子显示出响应RNAPII减慢的独特剪接模式，表明剪接受到共转录RNA折叠的广泛影响。PCCR内3 '端的富集提出了一个有趣的假设，即RNA折叠和剪接之间的偶联可以介导过早的前mRNA切割和聚腺苷酸化的共转录抑制。RNA的二级结构对于前体mRNA的剪接、切割、多聚腺苷酸化和RNA编辑等加工过程具有重要的作用。在这里，作者通过定义预对齐的进化保守区域中的保守互补区域对（PCCR），呈现了人类转录组中保守的远程RNA结构目录。
The ability of nucleic acids to form double-stranded structures is essential for all living systems on Earth. Current knowledge on functional RNA structures is focused on locally-occurring base pairs. However, crosslinking and proximity ligation experiments demonstrated that long-range RNA structures are highly abundant. Here, we present the most complete to-date catalog of conserved complementary regions (PCCRs) in human protein-coding genes. PCCRs tend to occur within introns, suppress intervening exons, and obstruct cryptic and inactive splice sites. Double-stranded structure of PCCRs is supported by decreased icSHAPE nucleotide accessibility, high abundance of RNA editing sites, and frequent occurrence of forked eCLIP peaks. Introns with PCCRs show a distinct splicing pattern in response to RNAPII slowdown suggesting that splicing is widely affected by co-transcriptional RNA folding. The enrichment of 3’-ends within PCCRs raises the intriguing hypothesis that coupling between RNA folding and splicing could mediate co-transcriptional suppression of premature pre-mRNA cleavage and polyadenylation. Functional RNA secondary structure is important for the pre-mRNA processing including splicing, cleavage and polyadenylation, and RNA editing. Here the authors present a catalog of conserved long-range RNA structures in the human transcriptome by defining pairs of conserved complementary regions (PCCR) in pre-aligned evolutionarily conserved regions.
登录
查看更多内容
影响因子：
14.9
作者：
The Gene Ontology Consortium
通讯作者：
The Gene Ontology Consortium
Biopython：用于计算分子生物学和生物信息学的免费 Python 工具。
DOI：
10.1093/bioinformatics/btp163
发表时间：
2009-06-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Cock PJ;Antao T;Chang JT;Chapman BA;Cox CJ;Dalke A;Friedberg I;Hamelryck T;Kauff F;Wilczynski B;de Hoon MJ
通讯作者：
de Hoon MJ
影响因子：
5.8
作者：
Bretschneider, Hannes;Gandhi, Shreshth;Frey, Brendan J.
通讯作者：
Frey, Brendan J.
RIC-seq 用于 RNA–RNA 空间相互作用的全局原位分析
影响因子：
64.8
作者：
Cai, Zhaokui;Cao, Changchang;Xue, Yuanchao
通讯作者：
Xue, Yuanchao
RNA聚合酶II伸长在转录和替代剪接的十字路口。
影响因子：
--
作者：
de la Mata M;Muñoz MJ;Alló M;Fededa JP;Schor IE;Kornblihtt AR
通讯作者：
Kornblihtt AR