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Research: Arabidopsis retrotransposon virus-like particles and their regulation by epigenetically activated small RNA
- Seung Cho Lee,
- Evan Ernst,
- Benjamin Berube,
- Filipe Borges,
- Jean-Sebastien Parent,
- Paul Ledon,
- Andrea Schorn,
- and Robert A. Martienssen
Genome Res. April 2020 30: 576-588; Published in Advance April 17, 2020, doi:10.1101/gr.259044.119
..., and ddm1rdr6 is shown with |log2(fold-change)| ≥ 2 and FDR threshold at 5%. Each point corresponds to an annotated transposable element. Multiple ATHILA subfamilies were combined and labeled as “ATHILA.” (B) Coverage of short- and long-read VLP DNA-seq at representative LTR retrotransposon loci (EVADE, AT...
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Method: Identification of bona fide B2 SINE retrotransposon transcription through single-nucleus RNA-seq of the mouse hippocampus
- Sara B. Linker,
- Lynne Randolph-Moore,
- Kalyani Kottilil,
- Fan Qiu,
- Baptiste N. Jaeger,
- Jerika Barron,
- and Fred H. Gage
Genome Res. November 2020 30: 1643-1654; Published in Advance October 29, 2020, doi:10.1101/gr.262196.120
...this method to identify SINE activation in a context that is relevant for normal learning and memory.Retrotransposons are a class of transposable elements (TEs) that integrate into the host through an RNA intermediate (Craig et al. 2015). It is important to be able to examine the transcription of TE RNA...
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Research: Capture of a functionally active methyl-CpG binding domain by an arthropod retrotransposon family
- Alex de Mendoza,
- Jahnvi Pflueger,
- and Ryan Lister
Genome Res. August 2019 29: 1277-1286; Published in Advance June 25, 2019, doi:10.1101/gr.243774.118
...with silencing, we discovered that a family of arthropod Copia retrotransposons have incorporated a host-derived MBD. We functionally show how retrotransposon-encoded MBDs preferentially bind to CpG-dense methylated regions, which correspond to transposable element regions of the host , in the myriapod Strigamia...
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Research: A hot L1 retrotransposon evades somatic repression and initiates human colorectal cancer
- Emma C. Scott,
- Eugene J. Gardner,
- Ashiq Masood,
- Nelson T. Chuang,
- Paula M. Vertino,
- and Scott E. Devine
Genome Res. June 2016 26: 745-755; Published in Advance May 10, 2016, doi:10.1101/gr.201814.115
...show that L1 source profiles vary considerably depending on the ancestry of an individual, and that population-specific hot L1 elements represent a novel form of cancer risk.Human LINE-1 (L1) elements are autonomous retrotransposons that continue to produce new “offspring” L1 insertions in human s...
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Resource: Exploring the epigenome profiles of repetitive elements with the WashU Repeat Browser
- Jiawei Shen,
- Siyuan Cheng,
- Deepak Purushotham,
- Xiaoyu Zhuo,
- Alan Y Du,
- Wenjin Zhang,
- Daofeng Li,
- and Ting Wang
Genome Res. February 21, 2025 gr.279764.124; Published in Advance February 21, 2025, doi:10.1101/gr.279764.124
...of TEs. WashU Repeat Browser is a web-based platform allowing users to browse genomic and statistical signals over repetitive elements derived from ENCODE, Roadmap, and FANTOM datasets. The Browser provides a TE-centric view including TE subfamily enrichments, TE subfamily profiling, as well as overviews...
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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...for enrichment of transcriptional-inducing MPRA fragments within a TE superfamily compared with all other TEs. Unknown taxonomy and DNA/retrotransposons of unknown origin (DTX/RLX) are considered separate groups. A similar test is also done on the subfamily level, and the number of significant TE subfamilies...
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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
...-stimulated primary aortic endothelial cells isolated from human, mouse, and cow, we find that 55 TE subfamilies are associated with RELA-bound regions, many of which reside near TNF-responsive genes. A prominent example of lineage-specific contribution of transposons comes from the bovine SINE subfamilies Bov-tA1...
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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
...artifacts of incomplete transcripts derived from intronic SINEs (Fig. 1E; Supplemental Fig. S2A; Sela et al. 2007; Elbarbary et al. 2016; Shao and Wang 2021; Gualandi et al. 2022). Across all three transcript tiers, we observed similar subfamily enrichment, particularly with LTRs like ERV1, suggesting...
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Letter: Exon-trapping mediated by the human retrotransposon SVA
- Dustin C. Hancks,
- Adam D. Ewing,
- Jesse E. Chen,
- Katsushi Tokunaga,
- and Haig H. Kazazian, Jr
Genome Res. November 2009 19: 1983-1991; Published in Advance July 27, 2009, doi:10.1101/gr.093153.109
..., both inactive and active retrotransposons drive genome evolution and may influence transcription through various mechanisms. In humans, three retrotransposon families are still active, but one of these, SVA, remains mysterious. Here we report the identification of a new subfamily of SVA, which...
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LETTER: An extraordinary retrotransposon family encoding dual endonucleases
- Kenji K. Kojima and
- Haruhiko Fujiwara
Genome Res. August 2005 15: 1106-1117; doi:10.1101/gr.3271405
...-LTR retrotransposon in the fungal phytopathogen Colletotrichum gloeosporioides , S-D-H is substituted to A-D-H. Nonconserved residues are variable among the Dualen subfamilies. This indicates that there has been enough time to be mutated since Dualen acquired APE. If the APE domain of Dualen was inactive, other...

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