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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
...310022, China; 9State Key Laboratory for Macromolecule Drugs and Large-scale Manufacturing, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325030, China ↵10 These authors contributed equally to this work. Corresponding authors: wuyf@immunol.org, reny@genomics.cn, jingang...
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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
...of the signature RTEs were from L1, ERV1, ERVL, and Alu subfamilies (Fig. 3H), which is largely consistent with the number of copies of these subfamilies (Fig. 1A,B).Previous studies have highlighted the important role of L1s in diseased and healthy human brains. TDP-43 regulates genomic L1 accessibility...
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Research: Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding
- Liangxi Wang,
- Tiegh Taylor,
- Kumaragurubaran Rathnakumar,
- Nadiya Khyzha,
- Minggao Liang,
- Azad Alizada,
- Laura F. Campitelli,
- Sara E. Pour,
- Zain M. Patel,
- Lina Antounians,
- Ian C. Tobias,
- Huayun Hou,
- Timothy R. Hughes,
- Sushmita Roy,
- Jennifer A. Mitchell,
- Jason E. Fish,
- and Michael D. Wilson
Genome Res. July 2025 35: 1544-1559; Published in Advance June 6, 2025, doi:10.1101/gr.280357.124
.... Mitchell4, Jason E. Fish6,7,15 and Michael D. Wilson1,2 1Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3K3, Canada; 2Genetics and Genome Biology, SickKids Research Institute, Toronto, Ontario M5G 0A4, Canada; 3Institut de Pharmacologie Moléculaire et Cellulaire, Université...
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Research: Loss of epigenetic suppression of retrotransposons with oncogenic potential in aging mammary luminal epithelial cells
- Parijat Senapati,
- Masaru Miyano,
- Rosalyn W. Sayaman,
- Mudaser Basam,
- Amy Leung,
- Mark A. LaBarge,
- and Dustin E. Schones
Genome Res. August 2023 33: 1229-1241; Published in Advance July 18, 2023, doi:10.1101/gr.277511.122
...in bulk suggested a decline in methylation of Alu and HERV-K elements with age in human blood cells (Bollati et al. 2009; Jintaridth and Mutirangura 2010). Increased expression of retrotransposons and active retrotransposition has furthermore been reported in aging mouse tissues (De Cecco et al. 2013...
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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
...Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA; 3McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA ↵4 These authors contributed equally to this work. Corresponding...
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Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
..., and identified it to be a SINE–VNTR–Alu (SVA) retrotransposon element present in a mosaic state in the mother (Sabatella et al. 2021). A broader analysis of 120 previously unsolved families severely affected by breast, ovarian, pancreatic, or metastatic prostate cancer identified rare deep intronic variants...
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Method: Multisample motif discovery and visualization for tandem repeats
- Yaran Zhang,
- Marc Hulsman,
- Alex Salazar,
- Niccolò Tesi,
- Lydian Knoop,
- Sven van der Lee,
- Sanduni Wijesekera,
- Jana Krizova,
- Erik-Jan Kamsteeg,
- and Henne Holstege
Genome Res. April 2025 35: 850-862; Published in Advance November 13, 2024, doi:10.1101/gr.279278.124
...Yaran Zhang1, Marc Hulsman1,2, Alex Salazar1, Niccolò Tesi1,2, Lydian Knoop1, Sven van der Lee1,2,3, Sanduni Wijesekera1, Jana Krizova1, Erik-Jan Kamsteeg4 and Henne Holstege1,2,3,5 1Section Genomics of Neurodegenerative Diseases and Aging, Department of Clinical Genetics, Vrije Universiteit...
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Mini-Review: The additional diagnostic yield of long-read sequencing in undiagnosed rare diseases
- Giulia F. Del Gobbo and
- Kym M. Boycott
Genome Res. April 2025 35: 559-571; Published in Advance February 3, 2025, doi:10.1101/gr.279970.124
...assess sequence variants (single nucleotide variants [SNVs] or insertions/deletions <50 bp), with the added ability to detect certain copy number variants and some structural variants (SVs, genomic alterations >50 bp in size). Since its more widespread adoption, -wide SRS, primarily SR-ES, has emerged...
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Research: Alu insertion variants alter gene transcript levels
- Lindsay M. Payer,
- Jared P. Steranka,
- Maria S. Kryatova,
- Giacomo Grillo,
- Mathieu Lupien,
- Pedro P. Rocha,
- and Kathleen H. Burns
Genome Res. December 2021 31: 2236-2248; Published in Advance November 19, 2021, doi:10.1101/gr.261305.120
..., which included genomic context surrounding the Alu, we can distinguish between instances in which the Alu disrupts another regulator and those in which the Alu introduces new regulatory sequence. We next focused on three polymorphic Alu loci associated with breast cancer that display significant effects...
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Method: Characterizing tandem repeat complexities across long-read sequencing platforms with TREAT and otter
- Niccoló Tesi,
- Alex Salazar,
- Yaran Zhang,
- Sven van der Lee,
- Marc Hulsman,
- Lydian Knoop,
- Sanduni Wijesekera,
- Jana Krizova,
- Anne-Fleur Schneider,
- Maartje Pennings,
- Kristel Sleegers,
- Erik-Jan Kamsteeg,
- Marcel Reinders,
- and Henne Holstege
Genome Res. November 2024 34: 1942-1953; Published in Advance October 15, 2024, doi:10.1101/gr.279351.124
...Niccoló Tesi1,2,3,6, Alex Salazar1,6, Yaran Zhang1, Sven van der Lee1,2, Marc Hulsman1,2,3, Lydian Knoop1, Sanduni Wijesekera1, Jana Krizova1, Anne-Fleur Schneider1, Maartje Pennings4, Kristel Sleegers5, Erik-Jan Kamsteeg4, Marcel Reinders3 and Henne Holstege1,2,3 1Section Genomics...
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