Non-canonical RNA substrates of Drosha lack many of the conserved features found in primary microRNA stem-loops

Gu, K; Mok, L; Wakefield, MJ; Chong, MMW

Author(s): Gu, K; Mok, L; Wakefield, MJ; Chong, MMW;
Details: Publication Year 2024-03-20,Volume 14,Issue #1,Page 6713
Journal Title: Scientific Reports
Abstract: The RNase III enzyme Drosha has a central role in microRNA (miRNA) biogenesis, where it is required to release the stem-loop intermediate from primary (pri)-miRNA transcripts. However, it can also cleave stem-loops embedded within messenger (m)RNAs. This destabilizes the mRNA causing target gene repression and appears to occur primarily in stem cells. While pri-miRNA stem-loops have been extensively studied, such non-canonical substrates of Drosha have yet to be characterized in detail. In this study, we employed high-throughput sequencing to capture all polyA-tailed RNAs that are cleaved by Drosha in mouse embryonic stem cells (ESCs) and compared the features of non-canonical versus miRNA stem-loop substrates. mRNA substrates are less efficiently processed than miRNA stem-loops. Sequence and structural analyses revealed that these mRNA substrates are also less stable and more likely to fold into alternative structures than miRNA stem-loops. Moreover, they lack the sequence and structural motifs found in miRNA stem-loops that are required for precise cleavage. Notably, we discovered a non-canonical Drosha substrate that is cleaved in an inverse manner, which is a process that is normally inhibited by features in miRNA stem-loops. Our study thus provides valuable insights into the recognition of non-canonical targets by Drosha.
Publisher: Springer Nature
Keywords: Mice; Animals; *Ribonuclease III/metabolism; *MicroRNAs/metabolism; Proteins/metabolism; RNA, Messenger/genetics/metabolism; RNA Processing, Post-Transcriptional
Research Division(s): Bioinformatics
PubMed ID: 38509178
Publisher's Version: https://doi.org/10.1038/s41598-024-57330-5
Open Access at Publisher's Site: https://doi.org/10.1038/s41598-024-57330-5
Terms of Use/Rights Notice: Refer to copyright notice on published article.
Documents: s41598-024-57330-5.pdf - (4.95MB, application/pdf)

Creation Date: 2024-03-27 08:35:42

Last Modified: 2024-03-27 08:46:08