biostudies-literatureLi YSichuan University postdoctoral interdisciplinary Innovation Foundationthe 1·3·5 project for disciplines of excellence, West China Hospital, Sichuan UniversityNational Natural Science Foundation of ChinaSichuan Provincial Science and Technology Support ProgramSichuan Province Science and Technology Program482https://www.ebi.ac.uk/biostudies/studies/S-EPMC11909889biostudies-literatureUnknown25(1)<h4>Background</h4>Transposable elements (TEs), which constitute nearly half of the human genome, have long been regarded as genomic "dark matter". However, their reactivation in tumor cells, resulting in the production of TE-chimeric transcripts (TCTs), has emerged as a potential driver of cancer progression. The complexity and full extent of these transcripts remain elusive, largely due to the limitations of short-read next-generation sequencing technologies. These methods have struggled to comprehensively capture the diversity and structure of TCTs, particularly those involving short interspersed nuclear elements (SINEs) or closely co-transcribed TEs.<h4>Methods</h4>Leveraging full-length cDNA sequencing technology based on nanopore sequencing platform, we developed a customized pipelinBMC cancerLong-read RNA sequencing enables full-length chimeric transcript annotation of transposable elements in lung adenocarcinoma.PMC119098892024NSFSC11872022NSFSC1762ZYYC230242022NSFSC1553322005082022SCU1204582173383Liu YXie DLi YXie YXia LWang HWang YWang JfalseLong-read RNA sequencing enables full-length chimeric transcript annotation of transposable elements in lung adenocarcinoma.<h4>Background</h4>Transposable elements (TEs), which constitute nearly half of the human genome, have long been regarded as genomic "dark matter". However, their reactivation in tumor cells, resulting in the production of TE-chimeric transcripts (TCTs), has emerged as a potential driver of cancer progression. The complexity and full extent of these transcripts remain elusive, largely due to the limitations of short-read next-generation sequencing technologies. These methods have struggled to comprehensively capture the diversity and structure of TCTs, particularly those involving short interspersed nuclear elements (SINEs) or closely co-transcribed TEs.<h4>Methods</h4>Leveraging full-length cDNA sequencing technology based on nanopore sequencing platform, we developed a customized pipelin2025-01-01T00:00:00Z2025 Mar2026-06-01T22:55:15.283Z2025-04-06T10:50:29.655ZS-EPMC119098894008971910.1186/s12885-025-13888-5