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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
...correspond to primordial germ cells (PGCs) or multipotent stem cells. Consistently, the TFI/TFII subfamily monomer sequence and Donor 2 (see below) also showed partial demethylation in embryo AB15 (Fig. 2E). We also analyzed the methylation status of unfixed polymorphic insertions polyL1Tf_3 and polyL1Tf_4...
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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
...retrotransposon subfamily activation in the early embryo, followed by repression in adult tissues. These data highlight endogenous macaque L1 retrotransposition potential, provide prototypical evidence of L1-mediated somatic mosaicism in a nonhuman primate, and allude to L1 mobility in the brain over the past 30...
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Research: Pedigree-based estimation of human mobile element retrotransposition rates
- Julie Feusier,
- W. Scott Watkins,
- Jainy Thomas,
- Andrew Farrell,
- David J. Witherspoon,
- Lisa Baird,
- Hongseok Ha,
- Jinchuan Xing,
- and Lynn B. Jorde
Genome Res. October 2019 29: 1567-1577; doi:10.1101/gr.247965.118
...-exome sequencing (WES) (Gardner et al. 2018), there has not yet been a rigorous empirical study of heritable retrotransposition and retrotranspositional timing in multigenerational pedigrees. Moreover, it is unknown whether human germline retrotransposition is affected by the parent's age or sex, or whether...
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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 mobilization is tightly regulated in most cell types and developmental contexts, with CpG methylation of the L1 internal promoter representing a key mechanism for control of L1 activity (Goodier and Kazazian 2008). In the mammalian germline and early embryo, L1 escapes repression to mobilize and create...
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Research: Retrotransposition creates sloping shores: a graded influence of hypomethylated CpG islands on flanking CpG sites
- Fiorella C. Grandi,
- James M. Rosser,
- Simon J. Newkirk,
- Jun Yin,
- Xiaoling Jiang,
- Zhuo Xing,
- Leanne Whitmore,
- Sanum Bashir,
- Zoltán Ivics,
- Zsuzsanna Izsvák,
- Ping Ye,
- Y. Eugene Yu,
- and Wenfeng An
Genome Res. August 2015 25: 1135-1146; Published in Advance May 20, 2015, doi:10.1101/gr.185132.114
...of retrotransposition on genomic structure and function is not limited to the germline . Recent -wide or targeted sequencing efforts indicate that somatic retrotransposition appears to be more rampant than in the germline, creating mosaic somatic s in cancer and neuronal cells (Babatz and Burns 2013; Reilly et al. 2013...
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Research: Locus- and domain-dependent control of DNA methylation at mouse B1 retrotransposons during male germ cell development
- Kenji Ichiyanagi,
- Yungfeng Li,
- Toshiaki Watanabe,
- Tomoko Ichiyanagi,
- Kei Fukuda,
- Junko Kitayama,
- Yasuhiro Yamamoto,
- Satomi Kuramochi-Miyagawa,
- Toru Nakano,
- Yukihiro Yabuta,
- Yoshiyuki Seki,
- Mitinori Saitou,
- and Hiroyuki Sasaki
Genome Res. December 2011 21: 2058-2066; Published in Advance October 31, 2011, doi:10.1101/gr.123679.111
.... In contrast, it is modifiable in early embryos and germ cells. Primordial germ cells (PGCs) undergo extensive erasure of methylation (Hajkova et al. 2002; Seki et al. 2005), and in males, prospermatogonia (gonocytes) acquire newmethylationmarks (Sasaki and Matsui 2008) (for stages during male germ cell...
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Resource: Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression
- Ni-Chen Chang,
- Quirze Rovira,
- Jonathan Wells,
- Cédric Feschotte,
- and Juan M. Vaquerizas
Genome Res. July 2022 32: 1408-1423; Published in Advance January 5, 2022, doi:10.1101/gr.275655.121
....vaquerizas@lms.mrc.ac.ukAbstractThere is considerable interest in understanding the effect of transposable elements (TEs) on embryonic development. Studies in humans and mice are limited by the difficulty of working with mammalian embryos and by the relative scarcity of active TEs in these organisms. The zebrafish is an outstanding model...
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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: Human postmeiotic sex chromatin and its impact on sex chromosome evolution
- Ho-Su Sin,
- Yosuke Ichijima,
- Eitetsu Koh,
- Mikio Namiki,
- and Satoshi H. Namekawa
Genome Res. May 2012 22: 827-836; Published in Advance February 28, 2012, doi:10.1101/gr.135046.111
...is available for this article.] The germline is the only heritable lineage across generations and drives evolution. In themale germline, X andY chromosomes exist in hemizygosity and are vulnerable to genetic exchanges (Vicoso and Charlesworth 2006; Ellegren 2011). Therefore, the genetic contents of sex...

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