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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 expression in neurons (Liu et al. 2019; Copley and Shorter 2023) and is widely observed to accumulate in neurodegenerative diseases (Jo et al. 2020). Genome-wide L1 insertion studies of neurons in the healthy human brain suggested that neuronal L1s might contribute to phytopathology and susceptibility...
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Research: Ruminant-specific retrotransposons shape regulatory evolution of bovine immunity
- Conor J. Kelly,
- Carol G. Chitko-McKown,
- and Edward B. Chuong
Genome Res. August 2022 32: 1474-1486; Published in Advance August 10, 2022, doi:10.1101/gr.276241.121
...across cetruminant lineages.Next, we examined the evolutionary history of Bov-A2 elements, which our analysis identified as another major source of predicted IFNG-inducible enhancers. Bov-A2 elements are SINE-like elements derived from the BovB retrotransposon roughly 20–40 mya and constitute one...
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Research: Independent expansion, selection, and hypervariability of the TBC1D3 gene family in humans
- Xavi Guitart,
- David Porubsky,
- DongAhn Yoo,
- Max L. Dougherty,
- Philip C. Dishuck,
- Katherine M. Munson,
- Alexandra P. Lewis,
- Kendra Hoekzema,
- Jordan Knuth,
- Stephen Chang,
- Tomi Pastinen,
- and Evan E. Eichler
Genome Res. November 2024 34: 1798-1810; Published in Advance August 6, 2024, doi:10.1101/gr.279299.124
...the TBC1D3 loci (Liao et al. 2023; Makova et al. 2024; Mao et al. 2024). The goals of this study were to reconstruct the evolutionary history of this gene family, to assess the extent of human genetic diversity, and to determine how this variation relates to changes in selection and expression of the gene...
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Research: ZNF91 deletion in human embryonic stem cells leads to ectopic activation of SVA retrotransposons and up-regulation of KRAB zinc finger gene clusters
- Nina L. Haring,
- Elisabeth J. van Bree,
- Whitney S. Jordaan,
- Judith R.E. Roels,
- Gonzalo Congrains Sotomayor,
- Tiziana M. Hey,
- Fred T.G. White,
- Marc D. Galland,
- Marten P. Smidt,
- and Frank M.J. Jacobs
Genome Res. April 2021 31: 551-563; Published in Advance March 15, 2021, doi:10.1101/gr.265348.120
...contributed an extra layer of species-specific gene regulation by providing novel transcription factor binding sites. In humans, SINE-VNTR-Alu (SVA) elements are one of three still active TE families; approximately 2800 SVA insertions exist in the human , half of which are human-specific. TEs are often...
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Research: The HUSH complex cooperates with TRIM28 to repress young retrotransposons and new genes
- Luisa Robbez-Masson,
- Christopher H.C. Tie,
- Lucia Conde,
- Hale Tunbak,
- Connor Husovsky,
- Iva A. Tchasovnikarova,
- Richard T. Timms,
- Javier Herrero,
- Paul J. Lehner,
- and Helen M. Rowe
Genome Res. May 4, 2018 ; Published in Advance May 4, 2018, doi:10.1101/gr.228171.117
...Centre, UCL Cancer Institute, University College London, London WC1E 6DD, United Kingdom; 3Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom Retrotransposons encompass half of the human and contribute to the formation of heterochromatin, which provides...
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Research: The life history of retrocopies illuminates the evolution of new mammalian genes
- Francesco Nicola Carelli,
- Takashi Hayakawa,
- Yasuhiro Go,
- Hiroo Imai,
- Maria Warnefors,
- and Henrik Kaessmann
Genome Res. March 2016 26: 301-314; Published in Advance January 4, 2016, doi:10.1101/gr.198473.115
...of retroposition (retroduplication), where RNAs are reverse-transcribed into DNA and inserted into the (Kaessmannet al. 2009). This process,which inmammals is accomplished by the LINE-1 retrotransposon machinery (Esnault et al. 2000), typically generates gene copies (retrocopies) devoid of introns and promoters...
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Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
- Jacopo Martelossi,
- Jacopo Vujovic,
- Yue Huang,
- Alessia Tatti,
- Kaiwei Xu,
- Federico Puliga,
- Yuanxue Chen,
- Omar Rota Stabelli,
- Fabrizio Ghiselli,
- Xiaoping Zhang,
- and Alessandra Zambonelli
Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
....001) (Supplemental Fig. S5). TE hotspots are richer in long retrotransposon insertions, whereas DNA elements are predominant transposons in TE coldspots (Supplemental Fig. S6). Moreover, the latter genomic compartment contains almost all PCGs (7047), with a gene density of 0.32, 2.6 times higher than the -wide...
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Research: Birth of protein-coding exons by ancient domestication of LINE-1 retrotransposon
- Koichi Kitao,
- Kenji Ichiyanagi,
- and So Nakagawa
Genome Res. June 2025 35: 1287-1300; Published in Advance May 8, 2025, doi:10.1101/gr.280007.124
...examples of L1 co-option for vertebrate proteins have been reported. Here, we describe protein isoforms, in which the L1 retrotransposons are incorporated into host genes as protein-coding exons by alternative splicing. L1 ORF1 protein (ORF1p) is an RNA-binding protein that binds to L1 RNA and is required...
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Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
...Aparecida Carareto1 1São Paulo State University (Unesp), Institute of Biosciences, Humanities and Exact Sciences, São José do Rio Preto, São Paulo 15054-000, Brazil; 2Université Claude Bernard Lyon 1, Laboratoire de Biométrie et Biologie Évolutive, CNRS, UMR5558, Villeurbanne 69100, France; 3Department...
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Research: Continuous infiltration and evolutionary trajectory of nuclear organelle DNA in Oryza
- Chenbo Gong,
- Yicheng Huang,
- Mengmeng Liu,
- Yong Zhou,
- Yinwei Xu,
- Nahed Mohammed,
- Xintong Qiao,
- Andrea Zuccolo,
- Weibo Xie,
- Rod A. Wing,
- Jianwei Zhang,
- Fei Zhou,
- and Yongjun Lin
Genome Res. June 2025 35: 1349-1363; Published in Advance April 25, 2025, doi:10.1101/gr.279609.124
...approximately once in every 4000 births (Wei et al. 2022), with a higher rate in cancer cells (Ju et al. 2015; Wei et al. 2022), leading to high NUMT diversity across the human population. The insertion of mtDNA into the nuclear can cause genomic instability via mutations or disruption of normal gene function...

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