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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
...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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Method: The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology
- Eugene J. Gardner,
- Vincent K. Lam,
- Daniel N. Harris,
- Nelson T. Chuang,
- Emma C. Scott,
- W. Stephen Pittard,
- Ryan E. Mills,
- The 1000 Genomes Project Consortium,
- and Scott E. Devine
Genome Res. November 2017 27: 1916-1929; Published in Advance August 30, 2017, doi:10.1101/gr.218032.116
...MEI is inverted relative to the 3′ portion). These 5′ inversions have been proposed to be caused by a mechanism termed “twin priming,” whereby the TPRT process is initiated simultaneously from both strands of DNA at the genomic integration site (Ostertag and Kazazian 2001). Another feature of these 5′ inverted L1...
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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
...) with the sequence 5′-CACTTGATAGTTTT-3′ (Fig. 1A; Supplemental Table S1). The insertion is truncated at the 5′ end and also contains a 5′ inversion and a small internal deletion at the inversion junction that presumably were caused by twin priming (Ostertag and Kazazian 2001). PCR validation assays confirmed...
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LETTER: L1 integration in a transgenic mouse model
- Daria V. Babushok,
- Eric M. Ostertag,
- Christine E. Courtney,
- Janice M. Choi,
- and Haig H. Kazazian, Jr.
Genome Res. February 2006 16: 240-250; Published in Advance December 19, 2005, doi:10.1101/gr.4571606
...by the exclusion from that study of elements with deletions &gt;51 nts. In our study, two of the elements contained a dual inverted fragment, likely generated by two consecutive twin priming attempts (see Extra Nucleotide Formation). These are distinct from previously reported multiple inversions comprised...
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LETTER: Novel retrotransposon analysis reveals multiple mobility pathways dictated by hosts
- Kenji Ichiyanagi,
- Ryo Nakajima,
- Masaki Kajikawa,
- and Norihiro Okada
Genome Res. January 2007 17: 33-41; Published in Advance December 6, 2006, doi:10.1101/gr.5542607
....M. , Kazazian, H.H. , Jr. ( 2001 ) Twin priming: A proposed mechanism for the creation of inversions in L1 retrotransposition . Genome Res. 11 : 2059 – 2065 . ↵ Roth, D.B. , Porter, T.N. , Wilson, J.H. ( 1985 ) Mechanisms of nonhomologous recombination in mammalian cells . Mol. Cell. Biol. 5 : 2599 – 2607...
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Resource: Whole-genome resequencing allows detection of many rare LINE-1 insertion alleles in humans
- Adam D. Ewing and
- Haig H. Kazazian, Jr.
Genome Res. June 2011 21: 985-990; Published in Advance October 27, 2010, doi:10.1101/gr.114777.110
..., Kazazian HH Jr. 2001. Twin priming: A proposed mechanism for the creation of inversions in L1 retrotransposition. Genome Res 11: 2059–2065. Quinlan AR, Clark RA, Sokolova S, Leibowitz ML, Zhang Y, Hurles ME, Mell JC, Hall IM. 2010. Genome-wide mapping and assembly of structural variant breakpoints...
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Letter: Mobile elements create structural variation: Analysis of a complete human genome
- Jinchuan Xing,
- Yuhua Zhang,
- Kyudong Han,
- Abdel Halim Salem,
- Shurjo K. Sen,
- Chad D. Huff,
- Qiong Zhou,
- Ewen F. Kirkness,
- Samuel Levy,
- Mark A. Batzer,
- and Lynn B. Jorde
Genome Res. September 2009 19: 1516-1526; Published in Advance May 13, 2009, doi:10.1101/gr.091827.109
...after the human–chimpanzee divergence (Hedges et al. 2004). For the 52 L1 insertions, in addition to the signatures of canonical retrotransposition, other typical structures associatedwith L1 insertions were identified: 11 insertions are inverted in the middle, presumably via the ‘‘twin-priming...
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REVIEW: Mammalian non-LTR retrotransposons: For better or worse, in sickness and in health
- Victoria P. Belancio,
- Dale J. Hedges,
- and Prescott Deininger
Genome Res. March 2008 18: 343-358; Published in Advance February 6, 2008, doi:10.1101/gr.5558208
...—or otherwise noteworthy—phenotypic variation. Some of the most highly publicized discoveries of this nature are the species-specific restriction of HIV infection in owl monkeys ( Sayah et al. 2004 ), the generation of merle coat patterns in dogs ( Clark et al. 2006 ), and the creation of new varieties...
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Letter: 5′-Transducing SVA retrotransposon groups spread efficiently throughout the human genome
- Annette Damert,
- Julija Raiz,
- Axel V. Horn,
- Johannes Löwer,
- Hui Wang,
- Jinchuan Xing,
- Mark A. Batzer,
- Roswitha Löwer,
- and Gerald G. Schumann
Genome Res. November 2009 19: 1992-2008; Published in Advance August 3, 2009, doi:10.1101/gr.093435.109
...that such structures are the consequence of a twin-priming mechanism by which 59-inverted elements are formed (Ostertag and Kazazian 2001). Clearly, members of transduction group 4 are a consequence of 39-transducing transcription of source element H10_1 and subsequent 59 truncation occurring during reverse...

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