Identification of the cross-strand chimeric RNAs generated by fusions of bi-directional transcripts

• Published in: Nature communications Vol. 12; no. 1; p. 4645
• Main Authors: Wang, Yuting, Zou, Qin, Li, Fajin, Zhao, Wenwei, Xu, Hui, Zhang, Wenhao, Deng, Haiteng, Yang, Xuerui
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 30-07-2021; Nature Publishing Group; Nature Portfolio
• Subjects: 38/39; 45/91; 631/114/2164; 631/1647/48; 631/337/2019; Alternative splicing; Antisense DNA; Deoxyribonucleic acid; DNA; Gene fusion; Gene sequencing; Genes; Humanities and Social Sciences; multidisciplinary; Polls & surveys; Ribonucleic acid; RNA; Science; Science (multidisciplinary); Splicing; Strands; Tissue analysis; Transcription; Transcriptomes
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-021-24910-2

A major part of the transcriptome complexity is attributed to multiple types of DNA or RNA fusion events, which take place within a gene such as alternative splicing or between different genes such as DNA rearrangement and trans-splicing. In the present study, using the RNA deep sequencing data, we systematically survey a type of non-canonical fusions between the RNA transcripts from the two opposite DNA strands. We name the products of such fusion events cross-strand chimeric RNA (cscRNA). Hundreds to thousands of cscRNAs can be found in human normal tissues, primary cells, and cancerous cells, and in other species as well. Although cscRNAs exhibit strong tissue-specificity, our analysis identifies thousands of recurrent cscRNAs found in multiple different samples. cscRNAs are mostly originated from convergent transcriptions of the annotated genes and their anti-sense DNA. The machinery of cscRNA biogenesis is unclear, but the cross-strand junction events show some features related to RNA splicing. The present study is a comprehensive survey of the non-canonical cross-strand RNA junction events, a resource for further characterization of the originations and functions of the cscRNAs.
Gene fusion, trans-splicing or transcription read-through contributes to generation of chimeric RNA. Here the authors develop a pipeline to identify non-canonical type of chimeric RNAs called cross-strand chimeric RNA (cscRNA), which are fused between two precursor RNAs transcribed from the opposite DNA strands.