BRIEF RESEARCH REPORT article
Front. Bioinform.
Sec. RNA Bioinformatics
Volume 5 - 2025 | doi: 10.3389/fbinf.2025.1575346
MORE-RNAseq: A pipeline for qualifying retrotransposition-capable LINE1 expression based on RNA-seq data
Provisionally accepted- 1Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Bunkyo-ku, Japan
- 2The Affiliated Mental Health Center, Jiangnan University, Wuxi, Liaoning Province, China
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Retrotransposon long interspersed nuclear element-1 (LINE-1, L1) consists of a large proportion of the mammalian genome. A fraction of L1s, which have no deleterious mutations in the structure, can amplify their copies via a process called retrotransposition (RT). RT affects genome stability and gene expression and is involved in the pathogenesis of many hereditary diseases. Measuring expression of RT-capable L1s (rc-L1s) among the hundreds of thousands of non rc-L1s is an essential step to understand the impact of RT. We developed mobile element-originated read enrichment from RNA-seq data (MORE-RNAseq), a pipeline for calculating expression of rc-L1s using manually curated L1 references in humans and mice. MORE-RNAseq allows for quantification of expression levels of overall (sum of the expression of all rc-L1s) and individual rc-L1s with consideration of the genomic context. We applied MORE-RNAseq to publicly available RNA-seq data of human and mouse cancer cell lines from the studies that reported increased L1 expression. We found the significant increase of rc-L1 expressions at the overall level in both inter-and intragenic contexts. We also identified differentially expressed rc-L1s at the locus level, which will be the important candidates for downstream analysis. We also applied our method to young and aged human muscle RNA-seq data with no prior information about L1 expression, and found a significant increase of rc-L1 expression in the aged samples. Our method will contribute to understand the role of rc-L1s in various physiological and pathophysiological conditions using standard RNA-seq data. All scripts are available at https://github.com/molbrain/MORE-RNAseq.
Keywords: LINE-1 (L1), Expression, RNA-Seq, Retrotransponson, transcription
Received: 12 Feb 2025; Accepted: 30 Apr 2025.
Copyright: © 2025 Nakachi, Du, Watanabe, Yanagida, Bundo and Iwamoto. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Kazuya Iwamoto, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, 113-8655, Bunkyo-ku, Japan
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