sRNAfrag: A pipeline and suite of tools to analyze fragmentation in small RNA sequencing data

• Type of Material: Article
• Authors: Ken Nakatsu, Emory University; Mayumi Jijiwa, University of Hwaii; Vedbar Khadka, University of Hawaii; Masaki Nasu, University of Hawaii; Matthew Huo, University of Hawaii; Youping Deng, University of Hawaii
• Language: English
• Date: 2023-08-21
• Publisher: NIH
• Publication Version: Preprint (Prior to Peer Review)
• Copyright Statement: The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
• License: Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International
• Final Published Version (URL): https://doi.org/10.1101%2F2023.08.19.553943
• Title of Journal or Parent Work: bioRxiv
• Grant/Funding Information: This research was funded by National Institutes of Health (NIH) grants R01CA230514, R01CA223490, U54GM138062, U54MD007601, P30GM114737, P20GM103466, P20GM139753, P30CA071789. This research was also funded by the Chun Foundation and the Jean Epstein Foundation.
• Keywords: Peaks; Conservation; fragments; snoRNA
• Research Categories: Biology, Molecular

Abstract

Fragments derived from small RNAs such as small nucleolar RNAs hold biological relevance. However, they remain poorly understood, calling for more comprehensive methods for analysis. We developed sRNAfrag, a standardized workflow and set of scripts to quantify and analyze sRNA fragmentation of any biotype. In a benchmark, it is able to detect loci of mature microRNAs fragmented from precursors and, utilizing multi-mapping events, the conserved 5’ seed sequence of miRNAs which we believe may extraoplate to other small RNA fragments. The tool detected 1411 snoRNA fragment conservation events between 2/4 eukaryotic species, providing the opportunity to explore motifs and fragmentation patterns not only within species, but between. Availability: https://github.com/kenminsoo/sRNAfrag.