4.7 Article

Reverse complementary matches simultaneously promote both back-splicing and exon-skipping

期刊

BMC GENOMICS
卷 22, 期 1, 页码 -

出版社

BMC
DOI: 10.1186/s12864-021-07910-w

关键词

Circular RNA; Back-splicing; Exon-skipping; reverse complementary matches; FACS

资金

  1. NIH Office of Research Infrastructure Programs [P40 OD010440]
  2. Scientific Computing and Data Analysis section of Research Support Division at OIST
  3. Okinawa Institute of Science and Technology, Graduate University

向作者/读者索取更多资源

This study obtained neuronal circRNA data in C. elegans through large-scale neuron isolation and RNA sequencing, revealing that circRNAs are highly expressed in neurons and positively correlated with their cognate linear mRNAs. Deletion of reverse complementary match (RCM) sequences in circRNA flanking introns effectively abolished circRNA formation. RCMs not only promote back-splicing but also facilitate exon-skipping, providing a new explanation for the correlation between the two processes.
Background Circular RNAs (circRNAs) play diverse roles in different biological and physiological environments and are always expressed in a tissue-specific manner. Especially, circRNAs are enriched in the brain tissues of almost all investigated species, including humans, mice, Drosophila, etc. Although circRNAs were found in C. elegans, the neuron-specific circRNA data is not available yet. Exon-skipping is found to be correlated to circRNA formation, but the mechanisms that link them together are not clear. Results Here, through large-scale neuron isolation from the first larval (L1) stage of C. elegans followed by RNA sequencing with ribosomal RNA depletion, the neuronal circRNA data in C. elegans were obtained. Hundreds of novel circRNAs were annotated with high accuracy. circRNAs were highly expressed in the neurons of C. elegans and were positively correlated to the levels of their cognate linear mRNAs. Disruption of reverse complementary match (RCM) sequences in circRNA flanking introns effectively abolished circRNA formation. In the zip-2 gene, deletion of either upstream or downstream RCMs almost eliminated the production of both the circular and the skipped transcript. Interestingly, the 13-nt RCM in zip-2 is highly conserved across five nematode ortholog genes, which show conserved exon-skipping patterns. Finally, through in vivo one-by-one mutagenesis of all the splicing sites and branch points required for exon-skipping and back-splicing in the zip-2 gene, I showed that back-splicing still happened without exon-skipping, and vice versa. Conclusions Through protocol optimization, total RNA obtained from sorted neurons is increased to hundreds of nanograms. circRNAs highly expressed in the neurons of C. elegans are more likely to be derived from genes also highly expressed in the neurons. RCMs are abundant in circRNA flanking introns, and RCM-deletion is an efficient way to knockout circRNAs. More importantly, these RCMs are not only required for back-splicing but also promote the skipping of exon(s) to be circularized. Finally, RCMs in circRNA flanking introns can directly promote both exon-skipping and back-splicing, providing a new explanation for the correlation between them.

作者

我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。

评论

主要评分

4.7
评分不足

次要评分

新颖性
-
重要性
-
科学严谨性
-
评价这篇论文

推荐

暂无数据
暂无数据