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Resource: Dynamic dysregulation of retrotransposons in neurodegenerative diseases at the single-cell level
- Wankun Deng,
- Citu Citu,
- Andi Liu,
- and Zhongming Zhao
Genome Res. October 2024 34: 1687-1699; Published in Advance October 18, 2024, doi:10.1101/gr.279363.124
...and Feschotte 2020). In humans, RTEs are further subdivided into long terminal repeats (LTRs) and non-LTRs, including long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs) (Li et al. 2022). However, LTRs and LINEs facilitate transposition by encoding their own reverse...
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Research: Loss of epigenetic suppression of retrotransposons with oncogenic potential in aging mammary luminal epithelial cells
- Parijat Senapati,
- Masaru Miyano,
- Rosalyn W. Sayaman,
- Mudaser Basam,
- Amy Leung,
- Mark A. LaBarge,
- and Dustin E. Schones
Genome Res. August 2023 33: 1229-1241; Published in Advance July 18, 2023, doi:10.1101/gr.277511.122
...and potentially impact disease risk. We describe here our investigation into the impact of aging on the epigenetic repression of TEs in normal mammary LEps, the primary suspected cell of origin for luminal breast cancers.ResultsEvolutionarily recent LTR elements function as regulatory elements in mammary LEps...
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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 stability.Retrotransposons are major contributors to ongoing mutagenesis in mammalian s. The autonomous non-long terminal repeat (non-LTR) retrotransposon Long Interspersed Element 1 (LINE-1 or L1) is actively mobilizing in both humans and mice, and L1 sequences occupy ∼17% of human DNA and ∼18% of mouse...
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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
...Gen) targeting the L1RS2, L1RS37, AluYRa4, AluYRb4, AluYRc2, AluYRd4, LTR14 (HERVK14), and LTR4 (MacERV1) subfamilies (Supplemental Table S1). The posthybridization library pool was then sequenced with paired-end 2 × 150 mer reads, using two flow cells of an Illumina HiSeq X platform (Macrogen...
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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
...Mammalian non-LTR retrotransposons: For better or worse, in sickness and in health Victoria P. Belancio , Dale J. Hedges , and Prescott Deininger 1 Tulane Cancer Center and Department of Epidemiology, Tulane University Health Sciences Center, New...
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LETTER: Active Alu retrotransposons in the human genome
- E. Andrew Bennett,
- Heiko Keller,
- Ryan E. Mills,
- Steffen Schmidt,
- John V. Moran,
- Oliver Weichenrieder,
- and Scott E. Devine
Genome Res. December 2008 18: 1875-1883; Published in Advance October 3, 2008, doi:10.1101/gr.081737.108
....J. ( 2000 ) Statistics with Confidence ( BMJ books , Bristol, UK ) 2d edition . ↵ Batzer, M.A. , Deininger, P.L. ( 2002 ) Alu repeats and human genomic diversity . Nat. Rev. Genet. 35 : 501 – 538 . ↵ Belancio, V.P. , Hedges, D.J. , Deininger, P. ( 2008 ) Mammalian non-LTR retrotransposons: For better...
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Research: Genome architecture marked by retrotransposons modulates predisposition to DNA methylation in cancer
- Marcos R.H. Estécio,
- Juan Gallegos,
- Céline Vallot,
- Ryan J. Castoro,
- Woonbok Chung,
- Shinji Maegawa,
- Yasuhiro Oki,
- Yutaka Kondo,
- Jaroslav Jelinek,
- Lanlan Shen,
- Helge Hartung,
- Peter D. Aplan,
- Bogdan A. Czerniak,
- Shoudan Liang,
- and Jean-Pierre J. Issa
Genome Res. October 2010 20: 1369-1382; Published in Advance August 17, 2010, doi:10.1101/gr.107318.110
...MCAMdata set for human cancers and found that LTRs are also depleted in methylation-prone genes, albeit to a lesser degree than SINE and LINE retrotransposons (Supplemental Fig. S3). However, adding LTR distribution to predict gene predisposition to DNA methylation in human cancer did not significantly improve...
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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
...; Elsik et al. 2009), including long interspersed elements (LINEs), short interspersed elements (SINEs), and long terminal repeat (LTR) retrotransposons (Deininger and Batzer 2002; Deininger et al. 2003). The activities of LINEs and LTR retrotransposons, which can act as aggressive mutators...
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Research: Dioxin receptor and SLUG transcription factors regulate the insulator activity of B1 SINE retrotransposons via an RNA polymerase switch
- Angel Carlos Román,
- Francisco J. González-Rico,
- Eduardo Moltó,
- Henar Hernando,
- Ana Neto,
- Cristina Vicente-Garcia,
- Esteban Ballestar,
- José L. Gómez-Skarmeta,
- Jana Vavrova-Anderson,
- Robert J. White,
- Lluís Montoliu,
- and Pedro M. Fernández-Salguero
Genome Res. March 2011 21: 422-432; Published in Advance February 3, 2011, doi:10.1101/gr.111203.110
...; Molto´ et al. 2009). It is known that transposable elements such as ERV1, ERVK, MIR1, LTR10, and MER61 contain binding sites for transcription factors (Wang et al. 2007; Bourque et al. 2008; Kuwabara et al. 2009; Kunarso et al. 2010). Moreover, a B2 SINE retrotransposon has been shown to insulate...
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Research: Accumulation and ineffective silencing of transposable elements on an avian W Chromosome
- Vera M. Warmuth,
- Matthias H. Weissensteiner,
- and Jochen B.W. Wolf
Genome Res. April 2022 32: 671-681; Published in Advance February 11, 2022, doi:10.1101/gr.275465.121
...; however, increasing evidence suggests that silencing of TEs is often incomplete. The crow family experienced a recent radiation of LTR retrotransposons (LTRs), offering an opportunity to gain insight into the regulatory control of young, potentially still active TEs. We quantified the abundance of TE...

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