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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
...(Schmidt et al. 2012; Wang et al. 2012). In mammals, TE-derived sequences contribute up to 40% of -wide binding sites for TFs located in TE-rich regions (Sundaram et al. 2014). It has been proposed that such co-option of TE-regulatory elements for gene regulatory networks can provide substantial...
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Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M Riley,
- Randa Elsayed,
- Mark D Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C Nelson
Genome Res. March 4, 2026 gr.280838.125; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...2 functional genomics approaches to identify highly conserved endodermal cis-regulatory 30 modules (CRMs) functioning across the 400 million years of evolution separating zebrafish 31 and humans. Our analyses suggest that there are few endoderm-specific CRMs, with many 32 CRMs governing pancreas...
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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
...1421, likely resulting from either tandem duplications and/or transposon-mediated sequence reshuffling (Supplemental Fig. S14).To further elucidate the mechanism underlying the rapid evolution of fbxn genes, we analyzed additional genes within the fbxn gene cluster region. Although most of these genes...
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Research: Functional characterization of enhancer activity during a long terminal repeat's evolution
- Alan Y. Du,
- Xiaoyu Zhuo,
- Vasavi Sundaram,
- Nicholas O. Jensen,
- Hemangi G. Chaudhari,
- Nancy L. Saccone,
- Barak A. Cohen,
- and Ting Wang
Genome Res. October 2022 32: 1840-1851; Published in Advance October 3, 2022, doi:10.1101/gr.276863.122
...identified LTR18A elements as potential enhancers in the human , primarily in epithelial cells. Together, our results provide a model for the origin, evolution, and co-option of TE-derived regulatory elements.Changes in gene regulation have long been implicated as crucial drivers in evolution (King...
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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
.... 2013. Endogenous retroviruses function as species-specific enhancer elements in the placenta. Nat Genet 45: 325–329. doi:10.1038/ng.2553 ↵Chuong EB, Elde NC, Feschotte C. 2016. Regulatory evolution of innate immunity through co-option of endogenous retroviruses. Science 351: 1083–1087. doi:10...
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Resource: Genetic features and genomic targets of human KRAB-zinc finger proteins
- Jonas de Tribolet-Hardy,
- Christian W. Thorball,
- Romain Forey,
- Evarist Planet,
- Julien Duc,
- Alexandre Coudray,
- Bara Khubieh,
- Sandra Offner,
- Cyril Pulver,
- Jacques Fellay,
- Michael Imbeault,
- Priscilla Turelli,
- and Didier Trono
Genome Res. August 2023 33: 1409-1423; Published in Advance September 20, 2023, doi:10.1101/gr.277722.123
...more than 400 million years ago. Previous work has revealed that many KZFPs recognize transposable element (TE)-embedded sequences as genomic targets, and that KZFPs facilitate the co-option of the regulatory potential of TEs for the benefit of the host. Here, we present a comprehensive survey...
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Research: Transposon wave remodeled the epigenomic landscape in the rapid evolution of X-Chromosome dosage compensation
- David C.H. Metzger,
- Imogen Porter,
- Brendan Mobley,
- Benjamin A. Sandkam,
- Lydia J.M. Fong,
- Andrew P. Anderson,
- and Judith E. Mank
Genome Res. November 2023 33: 1917-1931; Published in Advance November 21, 2023, doi:10.1101/gr.278127.123
...is important for understanding the molecular and evolutionary processes that regulate chromosome structure and gene regulatory processes (Dekker and Mirny 2016; Kuroda et al. 2016) and how the evolution of X-linked genes influences local adaptation (Lasne et al. 2017).The extensive analysis of dosage...
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Research: Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks
- Marta Farré,
- Jaebum Kim,
- Anastasia A. Proskuryakova,
- Yang Zhang,
- Anastasia I. Kulemzina,
- Qiye Li,
- Yang Zhou,
- Yingqi Xiong,
- Jennifer L. Johnson,
- Polina L. Perelman,
- Warren E. Johnson,
- Wesley C. Warren,
- Anna V. Kukekova,
- Guojie Zhang,
- Stephen J. O'Brien,
- Oliver A. Ryder,
- Alexander S. Graphodatsky,
- Jian Ma,
- Harris A. Lewin,
- and Denis M. Larkin
Genome Res. April 2019 29: 576-589; Published in Advance February 13, 2019, doi:10.1101/gr.239863.118
....Transcription factors often work in clusters to bind TFBSs within enhancers to regulate target genes (Bradley et al. 2010; Long et al. 2016). Also, changes in types of TFBSs within enhancers during the course of evolution may lead to changes in the corresponding enhancers’ regulatory activity and specificity (Long et...
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Research: Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes
- Vedran Franke,
- Sravya Ganesh,
- Rosa Karlic,
- Radek Malik,
- Josef Pasulka,
- Filip Horvat,
- Maja Kuzman,
- Helena Fulka,
- Marketa Cernohorska,
- Jana Urbanova,
- Eliska Svobodova,
- Jun Ma,
- Yutaka Suzuki,
- Fugaku Aoki,
- Richard M. Schultz,
- Kristian Vlahovicek,
- and Petr Svoboda
Genome Res. August 2017 27: 1384-1394; Published in Advance May 18, 2017, doi:10.1101/gr.216150.116
...that function as gene-remodeling platforms that stochastically sculpt gene expression and function in oocytes and zygotes. In comparison to enhancer evolution, LTR co-option presented here is more complex (involving simultaneous co-option of TSSs and SDs) and occurring at a large scale. Although fusion of ERVL...
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Resource: Impact of regulatory variation across human iPSCs and differentiated cells
- Nicholas E. Banovich,
- Yang I. Li,
- Anil Raj,
- Michelle C. Ward,
- Peyton Greenside,
- Diego Calderon,
- Po Yuan Tung,
- Jonathan E. Burnett,
- Marsha Myrthil,
- Samantha M. Thomas,
- Courtney K. Burrows,
- Irene Gallego Romero,
- Bryan J. Pavlovic,
- Anshul Kundaje,
- Jonathan K. Pritchard,
- and Yoav Gilad
Genome Res. January 2018 28: 122-131; Published in Advance December 5, 2017, doi:10.1101/gr.224436.117
..., consistent with previous work in embryonic stem cells (Fig. 2F; Kunarso et al. 2010), may allow for cell-type–specific evolution of the regulatory network by co-option of the transposed elements as regulatory elements, followed by fine-tuning through the selection of DNA mutations (Kunarso et al. 2010).While...
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