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Research: Transcriptomic landscape of transposable elements reveals LTR7-PLAAT4 as a potential oncogene and therapeutic target in pancreatic adenocarcinoma
- Meilong Shi,
- Chuanqi Teng,
- Shan Zhang,
- Xiaobo He,
- Lingyun Xu,
- Fengxian Han,
- Rongqi Wen,
- Ganjun Yu,
- Jingwen Liu,
- Yang Feng,
- Yanfeng Wu,
- Yan Ren,
- Gang Jin,
- and Jing Li
Genome Res. February 2026 36: 275-290; Published in Advance January 8, 2026, doi:10.1101/gr.280528.125
...of ∼27% (3/11). Two other TE-derived peptides, ETVTGVWSY and FLPDHWAVL, were similarly validated in AsPC-1 cells (Fig. 8D). To investigate their genomic and translational origins, we visualized the corresponding chimeric transcripts using the WashU Epi Browser. RNA-seq coverage and getorf-predicted open...
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Resource: Charting the regulatory landscape of TP53 on transposable elements in cancer
- Xuan Qu,
- Yonghao Liang,
- Colin McCornack,
- Xiaoyun Xing,
- Heather Schmidt,
- Chad Tomlinson,
- Catrina Fronick,
- Edward A. Belter, Jr.,
- Juan F. Macias-Velasco,
- and Ting Wang
Genome Res. June 2025 35: 1456-1471; Published in Advance May 13, 2025, doi:10.1101/gr.279398.124
...(Jang et al. 2019; Shah et al. 2023). Using a combination of SR-RNA-seq and LR-RNA-seq, we created a TE-derived transcript atlas, detailing TE loci with potential promoter activity in different TP53 expression and activation contexts. We found SR-RNA-seq, though robust in transcription quantification...
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Review: Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics
- Natan Belchikov,
- Justine Hsu,
- Xiang Jennie Li,
- Julien Jarroux,
- Wen Hu,
- Anoushka Joglekar,
- and Hagen U. Tilgner
Genome Res. November 2024 34: 1735-1746; doi:10.1101/gr.279640.124
...transcripts in a set of cells. By combining standard Illumina-based single-cell RNA-seq quantification of cultured cells’ transcriptomes with PacBio sequencing of the viral transcripts, it was found that this viral genetic variation explained part, but not all, of the heterogeneity in viral gene expression...
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Resource: Dynamic dysregulation of retrotransposons in neurodegenerative diseases at the single-cell level
- Wankun Deng,
- Citu Citu,
- Andi Liu,
- and Zhongming Zhao
Genome Res. October 2024 34: 1687-1699; Published in Advance October 18, 2024, doi:10.1101/gr.279363.124
...(2021) developed a pipeline to quantify RTEs at the transcript level, whereas scTE (He et al. 2021) and IRescue (Polimeni et al. 2024) provide subfamily level quantification of RTEs. Additionally, several tools, including SoloTE (Rodríguez-Quiroz and Valdebenito-Maturana 2022), MATES (Wang et al. 2024...
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Perspective: Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
- Ezequiel Calvo-Roitberg,
- Rachel F. Daniels,
- and Athma A. Pai
Genome Res. November 2024 34: 1719-1734; doi:10.1101/gr.279559.124
...are the gold standard for high-throughput transcriptome profiling (Wang et al. 2009). RNA-sequencing (RNA-seq) has been used to investigate gene expression (The ENCODE Project Consortium 2012), canonical and alternative mRNA splicing (Wright et al. 2022a), noncoding RNAs, and post-transcriptional modifications...
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Resource: Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations
- Wenyu Zhang,
- Anja Guenther,
- Yuanxiao Gao,
- Kristian Ullrich,
- Bruno Huettel,
- Aftab Ahmad,
- Lei Duan,
- Kaizong Wei,
- and Diethard Tautz
Genome Res. November 2024 34: 2118-2132; Published in Advance September 17, 2024, doi:10.1101/gr.279166.124
...et al. 2016; Kuo et al. 2017), our optimized approach improved the performance to enrich genuine full-length transcripts.Our overall results confirm the conclusions from previous studies that the diversity of alternatively spliced isoforms surpasses the current annotation level, even of exceptionally...
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Research: Differences in activity and stability drive transposable element variation in tropical and temperate maize
- Shujun Ou,
- Armin Scheben,
- Tyler Collins,
- Yinjie Qiu,
- Arun S. Seetharam,
- Claire C. Menard,
- Nancy Manchanda,
- Jonathan I. Gent,
- Michael C. Schatz,
- Sarah N. Anderson,
- Matthew B. Hufford,
- and Candice N. Hirsch
Genome Res. August 2024 34: 1140-1153; Published in Advance September 9, 2024, doi:10.1101/gr.278131.123
...be increased or reduced through retrotransposition or illegitimate recombination, respectively. LTR sequences proliferate via reverse transcription (Fedoroff 2012), and more active proliferation could increase relative family size in some s. Alternatively, intact LTR elements can be reduced to solo LTRs via...
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Resource: Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish
- Hyung Joo Lee,
- Yiran Hou,
- Ju Heon Maeng,
- Nakul M. Shah,
- Yujie Chen,
- Heather A. Lawson,
- Hongbo Yang,
- Feng Yue,
- and Ting Wang
Genome Res. July 2022 32: 1424-1436; Published in Advance June 1, 2022, doi:10.1101/gr.276052.121
...of noise at individual genomic sites.To address this issue, we used a transcript assembly approach that we recently developed (Modzelewski et al. 2021; Shao and Wang 2021). Briefly, we performed transcript assembly using all mapped RNA-seq reads and excluded all annotated protein-coding transcripts. We...
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Resource: Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression
- Ni-Chen Chang,
- Quirze Rovira,
- Jonathan Wells,
- Cédric Feschotte,
- and Juan M. Vaquerizas
Genome Res. July 2022 32: 1408-1423; Published in Advance January 5, 2022, doi:10.1101/gr.275655.121
...–TE transcripts is technically challenging, but long-read transcriptome sequencing will ease many of these difficulties and is therefore a promising avenue for future studies.Using bulk and single-cell RNA-seq to untangle temporal and lineage-specific patterns of TE expression, we observe broadly distinct...
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Research: Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain
- Christopher J. Playfoot,
- Julien Duc,
- Shaoline Sheppard,
- Sagane Dind,
- Alexandre Coudray,
- Evarist Planet,
- and Didier Trono
Genome Res. September 2021 31: 1531-1545; Published in Advance August 16, 2021, doi:10.1101/gr.275133.120
..., which identified widespread isoform diversity in human neurodevelopment (Jeffries et al. 2020). Advances in long-read sequencing technologies now enable de novo full-transcript assembly and isoform expression quantification, analyses challenging to perform with short-read RNA-seq approaches...
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