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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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Research: The evolution of duplicate gene expression in mammalian organs
- Katerina Guschanski,
- Maria Warnefors,
- and Henrik Kaessmann
Genome Res. September 2017 27: 1461-1474; Published in Advance July 25, 2017, doi:10.1101/gr.215566.116
...with the alternative definition of tissue specificity (tau) were the same, with the exception of mouse and human, where lineage-specific paralogs showed more placenta-specific expressed genes than expected. Expression evolution of mammalian duplicate genes Genome Research 1467 www..org specificity, the results were...
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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
...650223, China; 12Centre for Social Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark; 13Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russia; 14Guy Harvey Oceanographic Center, Halmos College...
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Resource: GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes
- Yi Shao,
- Chunyan Chen,
- Hao Shen,
- Bin Z. He,
- Daqi Yu,
- Shuai Jiang,
- Shilei Zhao,
- Zhiqiang Gao,
- Zhenglin Zhu,
- Xi Chen,
- Yan Fu,
- Hua Chen,
- Ge Gao,
- Manyuan Long,
- and Yong E. Zhang
Genome Res. April 2019 29: 682-696; Published in Advance March 12, 2019, doi:10.1101/gr.238733.118
..., including DNA- or RNA-mediated duplication and de novo origination, lead to a high rate of protein-coding gene gain in human evolution (Zhang et al. 2012; Zhang and Long 2014). Transcriptome profiling has revealed that new genes in the human postdating the human and mouse split (i.e., primate-specific genes...
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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
...or create new ones. Results Elementary features of ERVL LTRs MLT, MT, ORR1, and MT2 LTRs (collectively referred to as “ERVL LTRs” hereafter) provide a unique model of LTR evolution and co-option during the last 80 million years. These LTRs were organized into 19 subgroups (Supplemental Fig. S1A), in which...
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LETTER: Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution
- Deyou Zheng,
- Adam Frankish,
- Robert Baertsch,
- Philipp Kapranov,
- Alexandre Reymond,
- Siew Woh Choo,
- Yontao Lu,
- France Denoeud,
- Stylianos E. Antonarakis,
- Michael Snyder,
- Yijun Ruan,
- Chia-Lin Wei,
- Thomas R. Gingeras,
- Roderic Guigó,
- Jennifer Harrow,
- and Mark B. Gerstein
Genome Res. June 2007 17: 839-851; doi:10.1101/gr.5586307
...University, New Haven, Connecticut 06520, USA Abstract Arising from either retrotransposition or genomic duplication of functional genes, pseudogenes are “genomic fossils” valuable for exploring the dynamics and evolution of genes and s. Pseudogene identification is an important problem in computational...
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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
...vertebrate genomic data has enabled further computational detection of co-option, revealing more than 100 co-option events of gag and env genes (Wang and Han 2020). A comprehensive analysis has revealed that lineage-specific transcription factors have arisen recurrently in vertebrates through the co-option...
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Research: Regulation of endogenous retrovirus–derived regulatory elements by GATA2/3 and MSX2 in human trophoblast stem cells
- Cui Du,
- Jing Jiang,
- Yuzhuo Li,
- Miao Yu,
- Jian Jin,
- Shuai Chen,
- Hairui Fan,
- Todd S. Macfarlan,
- Bin Cao,
- and Ming-an Sun
Genome Res. February 2023 33: 197-207; Published in Advance February 17, 2023, doi:10.1101/gr.277150.122
...: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:10.1126/science.aad5497 ↵Chuong EB, Elde NC, Feschotte C. 2017. Regulatory activities of transposable elements: from conflicts...
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Research: Allelic diversification after transposable element exaptation promoted gsdf as the master sex determining gene of sablefish
- Amaury Herpin,
- Manfred Schartl,
- Alexandra Depincé,
- Yann Guiguen,
- Julien Bobe,
- Aurélie Hua-Van,
- Edward S. Hayman,
- Anna Octavera,
- Goro Yoshizaki,
- Krista M. Nichols,
- Giles W. Goetz,
- and J. Adam Luckenbach
Genome Res. August 2021 31: 1366-1380; Published in Advance June 28, 2021, doi:10.1101/gr.274266.120
...has prominent phenotypic consequences, or if many consecutive alterations in the DNA over longer time periods lead to phenotypic divergence. In the marine teleost, sablefish (Anoplopoma fimbria), complementary genomic and genetic studies led to the identification of a sex locus on the Y Chromosome...
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Research: Transposable elements are the primary source of novelty in primate gene regulation
- Marco Trizzino,
- YoSon Park,
- Marcia Holsbach-Beltrame,
- Katherine Aracena,
- Katelyn Mika,
- Minal Caliskan,
- George H. Perry,
- Vincent J. Lynch,
- and Christopher D. Brown
Genome Res. October 2017 27: 1623-1633; Published in Advance August 30, 2017, doi:10.1101/gr.218149.116
...retroviruses function as species-specific enhancer elements in the placenta. Nat Genet 45: 325–329. Chuong EB, Elde NC, Feschotte C. 2016. Regulatory evolution of innate immunity through co-option of endogenous retroviruses. Science 351: 1083–1087. Cohen CJ, Lock WM, Mager DL. 2009. Endogenous retroviral LTRs...
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