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Research: Birth of protein-coding exons by ancient domestication of LINE-1 retrotransposon
- Koichi Kitao,
- Kenji Ichiyanagi,
- and So Nakagawa
Genome Res. June 2025 35: 1287-1300; Published in Advance May 8, 2025, doi:10.1101/gr.280007.124
...dispensable and leads to its loss. Importantly, such evolutionary replacement has been proposed for the evolution of syncytin genes, which are derived from ERVs, another group of retrotransposons (Imakawa et al. 2015). Functional syncytin genes have different viral origins in mammalian lineages (Lavialle et...
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Method: Recalibrating differential gene expression by genetic dosage variance prioritizes functionally relevant genes
- Philipp Rentzsch,
- Aaron Kollotzek,
- Kaushik Ram Ganapathy,
- Pejman Mohammadi,
- and Tuuli Lappalainen
Genome Res. October 2025 35: 2316-2325; Published in Advance September 17, 2025, doi:10.1101/gr.280360.124
....lappalainen@scilifelab.seAbstractDifferential expression (DE) analysis is a widely used method for identifying genes that are functionally relevant for an observed phenotype or biological response. However, typical DE analysis includes selection of genes based on a threshold of fold change in expression under the implicit assumption that all genes...
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Resource: A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq
- Sophia C. Gaynor-Gillett,
- Lijun Cheng,
- Manman Shi,
- Jason Liu,
- Gaoyuan Wang,
- Megan Spector,
- Qiuyu Guo,
- Le Qi,
- Mary Flaherty,
- Martha Wall,
- Ahyeon Hwang,
- Mengting Gu,
- Zhanlin Chen,
- Yuhang Chen,
- PsychENCODE Consortium,
- Jennifer R. Moran,
- Jing Zhang,
- Donghoon Lee,
- Mark Gerstein,
- Daniel Geschwind,
- and Kevin P. White
Genome Res. August 2025 35: 1887-1901; Published in Advance July 11, 2025, doi:10.1101/gr.279584.124
...equally to this work. Corresponding author: sgillett@cornellcollege.eduAbstractGenome-wide association studies (GWASs) and expression analyses implicate noncoding regulatory regions as harboring risk factors for psychiatric disease, but functional characterization of these regions remains limited. Here...
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Method: Tissular chromatin-state cartography based on double-barcoded DNA arrays that capture unloaded PA-Tn5 transposase
- Maria Grazia Mendoza-Ferri,
- Gwendoline Lozachmeur,
- Maximilien Duvina,
- Laetitia Perret,
- Didier Merciris,
- Anne Gigout,
- and Marco Antonio Mendoza-Parra
Genome Res. July 2025 35: 1633-1645; Published in Advance May 13, 2025, doi:10.1101/gr.280305.124
...for capturing chromatin histone modification signatures across tissue sections by taking advantage of a double-barcoded DNA arrays design compatible with in situ Protein A–transposase Tn5 tagmentation. This approach has been validated in presence of fresh-frozen mouse brain tissues but also in decalcified...
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Method: Single-cell Rapid Capture Hybridization sequencing reliably detects isoform usage and coding mutations in targeted genes
- Hongke Peng,
- Jafar S. Jabbari,
- Luyi Tian,
- Changqing Wang,
- Yupei You,
- Chong Chyn Chua,
- Natasha S. Anstee,
- Noorul Amin,
- Andrew H. Wei,
- Nadia M. Davidson,
- Andrew W. Roberts,
- David C.S. Huang,
- Matthew E. Ritchie,
- and Rachel Thijssen
Genome Res. April 2025 35: 942-955; Published in Advance January 10, 2025, doi:10.1101/gr.279322.124
...in insufficient read coverage, thereby limiting our ability to perform mutation calling for specific genes. Here, we developed a single-cell Rapid Capture Hybridization sequencing (scRaCH-seq) method that demonstrates high specificity and efficiency in capturing targeted transcripts using long-read sequencing...
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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
...catalog of active LTR retrotransposons without the need for mapping transposition, as well as independent of genomic copy number. Linear replication intermediates of the functionally intact COPIA element EVADE revealed multiple central polypurine tracts (cPPTs), a feature shared with HIV in which c...
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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
...BonaFide-TEseq to examine SINE expression in the mouse hippocampus as a function of a brief exposure to a NE at single-neuron resolution. Together, these results show the utility of single-cell data for examining bona fide retrotransposon expression.ResultsDetection of bona fide SINE transcripts...
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Method: Accessible Region Conformation Capture (ARC-C) gives high-resolution insights into genome architecture and regulation
- Ni Huang,
- Wei Qiang Seow,
- Alex Appert,
- Yan Dong,
- Przemyslaw Stempor,
- and Julie Ahringer
Genome Res. February 2022 32: 357-366; Published in Advance December 21, 2021, doi:10.1101/gr.275669.121
...Accessible Region Conformation Capture (ARC-C) gives high-resolution insights into architecture and regulation Ni Huang1,2, Wei Qiang Seow1,2, Alex Appert1, Yan Dong1, Przemyslaw Stempor1 and Julie Ahringer1 1The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB2 1...
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Resource: A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells
- William K.M. Lai,
- Luca Mariani,
- Gerson Rothschild,
- Edwin R. Smith,
- Bryan J. Venters,
- Thomas R. Blanda,
- Prashant K. Kuntala,
- Kylie Bocklund,
- Joshua Mairose,
- Sarah N. Dweikat,
- Katelyn Mistretta,
- Matthew J. Rossi,
- Daniela James,
- James T. Anderson,
- Sabrina K. Phanor,
- Wanwei Zhang,
- Zibo Zhao,
- Avani P. Shah,
- Katherine Novitzky,
- Eileen McAnarney,
- Michael-C. Keogh,
- Ali Shilatifard,
- Uttiya Basu,
- Martha L. Bulyk,
- and B. Franklin Pugh
Genome Res. September 2021 31: 1663-1679; Published in Advance August 23, 2021, doi:10.1101/gr.275472.121
...milieu. However, antibody availability and reliability can be problematic, whereas epitope tagging can be impractical in many cases. To address these limitations, the Protein Capture Reagents Program (PCRP) generated over a thousand renewable monoclonal antibodies (mAbs) against human presumptive...
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Method: Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ
- Joseph W. Foley,
- Chunfang Zhu,
- Philippe Jolivet,
- Shirley X. Zhu,
- Peipei Lu,
- Michael J. Meaney,
- and Robert B. West
Genome Res. November 2019 29: 1816-1825; Published in Advance September 13, 2019, doi:10.1101/gr.234807.118
...were captured in JPEG format with the built-in camera and software of the ArcturusXT system. Photographs in Figure 3 and Supplemental Figure S29 were color-corrected to enhance contrast with the automatic “Stretch HSV” function in GNU Image Manipulation Program 2.8.20. All photographs were recompressed...
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