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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
...and epigenetic status, including DNA methylation of the monomeric units constituting young mouse L1 promoters. Locus-specific L1 methylation dynamics during development may therefore elucidate and explain spatiotemporal niches of endogenous retrotransposition but remain unresolved. Here, we interrogate...
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Research: L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis
- Stephanie N. Schauer,
- Patricia E. Carreira,
- Ruchi Shukla,
- Daniel J. Gerhardt,
- Patricia Gerdes,
- Francisco J. Sanchez-Luque,
- Paola Nicoli,
- Michaela Kindlova,
- Serena Ghisletti,
- Alexandre Dos Santos,
- Delphine Rapoud,
- Didier Samuel,
- Jamila Faivre,
- Adam D. Ewing,
- Sandra R. Richardson,
- and Geoffrey J. Faulkner
Genome Res. May 2018 28: 639-653; Published in Advance April 11, 2018, doi:10.1101/gr.226993.117
..., and one GF subfamily example. One of the TF insertions carried a 3′ transduction, allowing us to identify its donor L1 and to demonstrate that this full-length TF element retained retrotransposition capacity in cultured cancer cells. Using RC-seq, we also identified eight tumor-specific L1 insertions from...
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Research: Heritable L1 retrotransposition in the mouse primordial germline and early embryo
- Sandra R. Richardson,
- Patricia Gerdes,
- Daniel J. Gerhardt,
- Francisco J. Sanchez-Luque,
- Gabriela-Oana Bodea,
- Martin Muñoz-Lopez,
- J. Samuel Jesuadian,
- Marie-Jeanne H.C. Kempen,
- Patricia E. Carreira,
- Jeffrey A. Jeddeloh,
- Jose L. Garcia-Perez,
- Haig H. Kazazian, Jr.,
- Adam D. Ewing,
- and Geoffrey J. Faulkner
Genome Res. August 2017 27: 1395-1405; Published in Advance May 8, 2017, doi:10.1101/gr.219022.116
...DE. 2008. Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition. Genome Res 18: 869–880. Akagi K, Stephens RM, Li J, Evdokimov E, Kuehn MR, Volfovsky N, Symer DE. 2010. MouseIndelDB: a database integrating genomic indel polymorphisms that distinguish mouse strains...
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Letter: A novel active endogenous retrovirus family contributes to genome variability in rat inbred strains
- Yongming Wang,
- František Liška,
- Claudia Gosele,
- Lucie Šedová,
- Vladimír Křen,
- Drahomíra Křenová,
- Zoltán Ivics,
- Norbert Hubner,
- and Zsuzsanna Izsvák
Genome Res. January 2010 20: 19-27; Published in Advance November 3, 2009, doi:10.1101/gr.100073.109
...A novel active endogenous retrovirus family contributes to genome variability in rat inbred strains Yongming Wang 1 , 4 , František Liška 1 , 2 , 4 , Claudia Gosele 1 , Lucie Šedová 2 , Vladimír Křen 2 , Drahomíra Křenová 2...
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Method: High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes
- Adam D. Ewing and
- Haig H. Kazazian, Jr
Genome Res. September 2010 20: 1262-1270; Published in Advance May 20, 2010, doi:10.1101/gr.106419.110
...by the NIH and the Penn Genome Frontiers Institute (PGFI). References Akagi K, Li J, Stephens RM, Volfovsky N, Symer DE. 2008. Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition. Genome Res 18: 869–880. Ahn SM, Kim TH, Lee S, KimD, Ghang H, KimDS, Kim BC, Kim SY, Kim...
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Research: Mouse endogenous retroviruses can trigger premature transcriptional termination at a distance
- Jingfeng Li,
- Keiko Akagi,
- Yongjun Hu,
- Anna L. Trivett,
- Christopher J.W. Hlynialuk,
- Deborah A. Swing,
- Natalia Volfovsky,
- Tamara C. Morgan,
- Yelena Golubeva,
- Robert M. Stephens,
- David E. Smith,
- and David E. Symer
Genome Res. May 2012 22: 870-884; Published in Advance February 23, 2012, doi:10.1101/gr.130740.111
...and Department of Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA Abstract Endogenous retrotransposons have caused extensive genomic variation within mammalian species, but the functional implications of such mobilization are mostly unknown. We...
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Research: The rate and spectrum of new mutations in mice inferred by long-read sequencing
- Eugenio López-Cortegano,
- Jobran Chebib,
- Anika Jonas,
- Anastasia Vock,
- Sven Künzel,
- Peter D. Keightley,
- and Diethard Tautz
Genome Res. January 2025 35: 43-54; Published in Advance December 2, 2024, doi:10.1101/gr.279982.124
.... To study variation in the mutation rate among mouse strains, our experiment included MA lines of three different commonly used inbred mouse strains (C3H, C57BL/6, and FVB). We used PacBio HiFi technology to sequence four MA samples from each of the three strains after 8 to 15 generations of MA. To aid...
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Research: Epigenetic activation of meiotic recombination near Arabidopsis thaliana centromeres via loss of H3K9me2 and non-CG DNA methylation
- Charles J. Underwood,
- Kyuha Choi,
- Christophe Lambing,
- Xiaohui Zhao,
- Heïdi Serra,
- Filipe Borges,
- Joe Simorowski,
- Evan Ernst,
- Yannick Jacob,
- Ian R. Henderson,
- and Robert A. Martienssen
Genome Res. April 2018 28: 519-531; Published in Advance March 12, 2018, doi:10.1101/gr.227116.117
...promote noncrossover repair and gene conversion (Dooner 1986; Borts and Haber 1987). A. thaliana centromeric regions exhibit extensive structural variation, including within Gypsy retroelements (Kumekawa et al. 2000; Ito et al. 2007; Quadrana et al. 2016; Stuart et al. 2016), which may therefore suppress...
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Research: Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome
- Aaron R. Quinlan,
- Royden A. Clark,
- Svetlana Sokolova,
- Mitchell L. Leibowitz,
- Yujun Zhang,
- Matthew E. Hurles,
- Joshua C. Mell,
- and Ira M. Hall
Genome Res. May 2010 20: 623-635; Published in Advance March 22, 2010, doi:10.1101/gr.102970.109
...extensive DNA copy number variation (CNV) among human individuals (Iafrate et al. 2004; Sebat et al. 2004), numerous studies have extended this observation in scope and scale with increasingly powerful genomic tools. It is now widely recognized that structural variation (SV), which includes duplications...
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Letter: Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila
- Jian Lu and
- Andrew G. Clark
Genome Res. February 2010 20: 212-227; Published in Advance November 30, 2009, doi:10.1101/gr.095406.109
...; however, piRNAs may provide a shelter or Trojan horse for retrotransposons, allowing them to increase in frequency in a population by shielding the host from the deleterious consequences of retrotransposition. Footnotes ↵ 1 Corresponding author. E-mail ac347@cornell.edu ; fax (607) 255...

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