{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T15:47:53Z","timestamp":1753890473351,"version":"3.41.2"},"reference-count":28,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,5,22]],"date-time":"2025-05-22T00:00:00Z","timestamp":1747872000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Bioinform."],"abstract":"<jats:p>Retrotransposon long interspersed nuclear element-1 (LINE-1, L1) constitutes 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 <jats:ext-link>https:\/\/github.com\/molbrain\/MORE-RNAseq<\/jats:ext-link>.<\/jats:p>","DOI":"10.3389\/fbinf.2025.1575346","type":"journal-article","created":{"date-parts":[[2025,5,22]],"date-time":"2025-05-22T08:56:54Z","timestamp":1747904214000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["MORE-RNAseq: a pipeline for quantifying retrotransposition-capable LINE1 expression based on RNA-seq data"],"prefix":"10.3389","volume":"5","author":[{"given":"Yutaka","family":"Nakachi","sequence":"first","affiliation":[]},{"given":"Jianbin","family":"Du","sequence":"additional","affiliation":[]},{"given":"Risa","family":"Watanabe","sequence":"additional","affiliation":[]},{"given":"Yutaro","family":"Yanagida","sequence":"additional","affiliation":[]},{"given":"Miki","family":"Bundo","sequence":"additional","affiliation":[]},{"given":"Kazuya","family":"Iwamoto","sequence":"additional","affiliation":[]}],"member":"1965","published-online":{"date-parts":[[2025,5,22]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1016\/0022-2836(91)80057-2","article-title":"Composite of A and F-type 5\u2019 terminal sequences defines a subfamily of mouse LINE-1 elements","volume":"221","author":"Adey","year":"1991","journal-title":"J. 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