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University of Hong Kong

Genome Biol., Mar 26 2025, 26 (1) 72 | https://doi.org/10.1186/s13059-025-03522-9 LocusMasterTE: integrating long-read RNA sequencing improves locus-specific quantification of transposable element expression

Sojung Lee ^1,2, Jayne A Barbour ^1,2, Yee Man Tam ¹, Haocheng Yang ¹, Yuanhua Huang ^1,3, Jason W H Wong ^1,2,*

¹School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
²Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China
³Center for Translational Stem Cell Biology, Hong Kong Science and Technology Park, Hong Kong SAR, China

^*Corresponding author: correspondence to Jason W H Wong

Abstract

Transposable elements (TEs) can influence human diseases by disrupting genome integrity, yet their quantification has been challenging due to the repetitive nature of these sequences across the genome. We develop LocusMasterTE, a method that integrates long-read with short-read RNA-seq to increase the accuracy of TE expression quantification. By incorporating fractional transcript per million values from long-read sequencing data into an expectation-maximization algorithm, LocusMasterTE reassigns multi-mapped reads, enhancing accuracy in short-read-based TE quantification. We validate the method with simulated and human datasets. LocusMasterTE may give new insights into TE functions through precise quantification.

논문정보

형식Research article
게재일2025년 03월 (BRIC 등록일 2025-03-31)
연구진국외 연구진
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