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Research: Locus-resolution analysis of L1 regulation and retrotransposition potential in mouse embryonic development
- Patricia Gerdes,
- Dorothy Chan,
- Mischa Lundberg,
- Francisco J. Sanchez-Luque,
- Gabriela O. Bodea,
- Adam D. Ewing,
- Geoffrey J. Faulkner,
- and Sandra R. Richardson
Genome Res. September 2023 33: 1465-1481; Published in Advance October 5, 2023, doi:10.1101/gr.278003.123
..., Queensland 4072, Australia Corresponding authors: faulknergj@gmail.com, sandra.richardson@mater.uq.edu.auAbstractMice harbor ∼2800 intact copies of the retrotransposon Long Interspersed Element 1 (L1). The in vivo retrotransposition capacity of an L1 copy is defined by both its sequence integrity...
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Research: Somatic retrotransposition in the developing rhesus macaque brain
- Victor Billon,
- Francisco J. Sanchez-Luque,
- Jay Rasmussen,
- Gabriela O. Bodea,
- Daniel J. Gerhardt,
- Patricia Gerdes,
- Seth W. Cheetham,
- Stephanie N. Schauer,
- Prabha Ajjikuttira,
- Thomas J. Meyer,
- Cora E. Layman,
- Kimberly A. Nevonen,
- Natasha Jansz,
- Jose L. Garcia-Perez,
- Sandra R. Richardson,
- Adam D. Ewing,
- Lucia Carbone,
- and Geoffrey J. Faulkner
Genome Res. July 2022 32: 1298-1314; Published in Advance June 21, 2022, doi:10.1101/gr.276451.121
...was full length, belonged to the L1RS2 subfamily, integrated at a 5′-TATT/AT-3′ motif, and was flanked by a 16-bp TSD (Fig. 1F). These features were consistent with a bona fide L1 retrotransposition event (Moran et al. 1996; Jurka 1997). Capillary sequencing of the 3′ junction PCR products revealed a very...
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Research: LTRs activated by Epstein-Barr virus–induced transformation of B cells alter the transcriptome
- Amy Leung,
- Candi Trac,
- Hiroyuki Kato,
- Kevin R. Costello,
- Zhaoxia Chen,
- Rama Natarajan,
- and Dustin E. Schones
Genome Res. December 2018 28: 1791-1798; Published in Advance October 31, 2018, doi:10.1101/gr.233585.117
...feature of mammalian hepatocarcinogenesis. Genome Res 28: 639–653. doi:10.1101/gr.226993.117 ↵Shukla R, Upton KR, Muñoz-Lopez M, Gerhardt DJ, Fisher ME, Nguyen T, Brennan PM, Baillie JK, Collino A, Ghisletti S, et al. 2013. Endogenous retrotransposition activates oncogenic pathways in hepatocellular...
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Research: CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors
- Kosuke Hashimoto,
- Ana Maria Suzuki,
- Alexandre Dos Santos,
- Christophe Desterke,
- Agnese Collino,
- Serena Ghisletti,
- Emilie Braun,
- Alessandro Bonetti,
- Alexandre Fort,
- Xian-Yang Qin,
- Enrico Radaelli,
- Bogumil Kaczkowski,
- Alistair R.R. Forrest,
- Soichi Kojima,
- Didier Samuel,
- Gioacchino Natoli,
- Marie Annick Buendia,
- Jamila Faivre,
- and Piero Carninci
Genome Res. December 2015 25: 1812-1824; Published in Advance October 28, 2015, doi:10.1101/gr.191031.115
...hepatocarcinogenesis (Braconi et al. 2011; Spizzo et al. 2012).We have established a comprehensive map of promoters for ncRNAs actively transcribed in a large set of human HCCs as well as in the Mdr2 KO mouse model of HCC using CAGE. This unique resource provides a mammalian promoter map for liver cancer at single...
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Research: Transposon expression in the Drosophila brain is driven by neighboring genes and diversifies the neural transcriptome
- Christoph D. Treiber and
- Scott Waddell
Genome Res. November 2020 30: 1559-1569; Published in Advance September 24, 2020, doi:10.1101/gr.259200.119
...with a dashed box. See Supplemental Table S5 for complete list.Splicing into transposons is common and varies between strainsTransposons are highly variable between fly strains. We therefore analyzed three previously published mRNA sequencing data sets from other fly strains for chimeric transposon–gene m...
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Research: Distinct contributions of DNA methylation and histone acetylation to the genomic occupancy of transcription factors
- Martin Cusack,
- Hamish W. King,
- Paolo Spingardi,
- Benedikt M. Kessler,
- Robert J. Klose,
- and Skirmantas Kriaucionis
Genome Res. October 2020 30: 1393-1406; Published in Advance September 22, 2020, doi:10.1101/gr.257576.119
...full-length members of the youngest L1 subfamilies, containing A-, TF-, or GF-type promoters are capable of retrotransposition, with the TF subtype being the most active in somatic cells and the germline (Akagi et al. 2008; Richardson et al. 2017; Schauer et al. 2018). Of the LINE-1 elements bound...
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Research: Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers
- David E. Symer,
- Keiko Akagi,
- Heather M. Geiger,
- Yang Song,
- Gaiyun Li,
- Anne-Katrin Emde,
- Weihong Xiao,
- Bo Jiang,
- André Corvelo,
- Nora C. Toussaint,
- Jingfeng Li,
- Amit Agrawal,
- Enver Ozer,
- Adel K. El-Naggar,
- Zoe Du,
- Jitesh B. Shewale,
- Birgit Stache-Crain,
- Mark Zucker,
- Nicolas Robine,
- Kevin R. Coombes,
- and Maura L. Gillison
Genome Res. January 2022 32: 55-70; Published in Advance December 13, 2021, doi:10.1101/gr.275911.121
...gene expression and maximum host gene expression in each tumor (Supplemental Fig. S4.2).Diverse forms of genetic disruption by HPV integrantsWe investigated relationships between HPV integrants and host genomic features such as annotated genes and regulatory elements. Consistent with previous findings...
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