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Research: Motif conservation, stability, and host gene expression are the main drivers of snoRNA expression across vertebrates
- Étienne Fafard-Couture,
- Pierre-Étienne Jacques,
- and Michelle S. Scott
Genome Res. April 2023 33: 525-540; Published in Advance April 18, 2023, doi:10.1101/gr.277483.122
...the role of these expression drivers in the evolution of snoRNA repertoires across vertebrate s.ResultsExpanding the characterization of features known to influence snoRNA expression to the whole human snoRNome challenges current knowledge on snoRNA biogenesisTo define the expression status of all human...
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Research: Evidence for compensatory evolution within pleiotropic regulatory elements
- Zane Kliesmete,
- Peter Orchard,
- Victor Yan Kin Lee,
- Johanna Geuder,
- Simon M. Krauß,
- Mari Ohnuki,
- Jessica Jocher,
- Beate Vieth,
- Wolfgang Enard,
- and Ines Hellmann
Genome Res. October 2024 34: 1528-1539; Published in Advance September 10, 2024, doi:10.1101/gr.279001.124
...Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109-2218, USA; 3Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, 1350 Copenhagen, Denmark; 4Department of Hematology, Cell Therapy, Hemostaseology and Infectious...
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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...The role of transposon activity in shaping cis-regulatory element evolution after whole- duplication Øystein Monsen1,6, Lars Grønvold1,6, Alex Datsomor1, Thomas Harvey1, James Kijas2, Alexander Suh3,4,7, Torgeir R. Hvidsten5 and Simen Rød Sandve1 1Department of Animal and Aquacultural Sciences...
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Research: Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary
- Satyam P. Srivastav,
- Cédric Feschotte,
- and Andrew G. Clark
Genome Res. May 2024 34: 711-724; Published in Advance May 15, 2024, doi:10.1101/gr.278062.123
...in Drosophila melanogaster, much less is known about the origin and evolution of piCs in this or any other species. To investigate piC origin and evolution, we use a population genomic approach to compare piC activity and sequence composition across eight geographically distant strains of D. melanogaster...
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Research: Transposable elements drive the evolution of metazoan zinc finger genes
- Jonathan N. Wells,
- Ni-Chen Chang,
- John McCormick,
- Caitlyn Coleman,
- Nathalie Ramos,
- Bozhou Jin,
- and Cédric Feschotte
Genome Res. August 2023 33: 1325-1339; Published in Advance September 15, 2023, doi:10.1101/gr.277966.123
...contributed equally to this work. Corresponding authors: jnw72@cornell.edu, cf458@cornell.eduAbstractCys2-His2 zinc finger genes (ZNFs) form the largest family of transcription factors in metazoans. ZNF evolution is highly dynamic and characterized by the rapid expansion and contraction of numerous...
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Research: GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes
- Anguo Liu,
- Nini Wang,
- Guoxiang Xie,
- Yang Li,
- Xixi Yan,
- Xinmei Li,
- Zhenliang Zhu,
- Zhuohui Li,
- Jing Yang,
- Fanxin Meng,
- Mingle Dou,
- Weihuang Chen,
- Nange Ma,
- Yu Jiang,
- Yuanpeng Gao,
- and Yu Wang
Genome Res. October 2023 33: 1673-1689; Published in Advance October 26, 2023, doi:10.1101/gr.277784.123
...-adjacent genes.To further explore the changes of ultraconservation along vertebrate evolution, we examined the conservation of our UCEs in all vertebrate taxa, including representatives of Reptilia, Amphibia, Osteichthyes, Chondrichthyes, and Cyclostomata (list in Supplemental Table S5). Most (>80%) mUCEs and a...
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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
...have a propensity to facilitate the evolution of certain biological processes, particularly those involving genetic conflicts. Studies investigating the epigenetic regulation of IFN responses in diverse vertebrate species may therefore uncover a widespread role for TEs in mediating the evolution...
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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
...revealed that LTR18A elements have generally lost regulatory activity over time through sequence changes, with the largest effects occurring owing to mutations in the AP-1 and CEBP motifs. We observed that the two motifs are conserved at higher rates than expected based on neutral evolution. Finally, we...
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Resource: The genomic architecture and molecular evolution of ant odorant receptors
- Sean K. McKenzie and
- Daniel J.C. Kronauer
Genome Res. November 2018 28: 1757-1765; Published in Advance September 24, 2018, doi:10.1101/gr.237123.118
.... This might be related to the greater gene numbers and/or potential similarities in gene regulation between ants and vertebrates as compared to flies.New genes provide abundant raw material for evolution to act upon and are likely instrumental in the phenotypic adaptation of organisms (Long et al. 2003, 2013...
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Research: Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution
- Florent Murat,
- Jian-Hong Xu,
- Eric Tannier,
- Michael Abrouk,
- Nicolas Guilhot,
- Caroline Pont,
- Joachim Messing,
- and Jérôme Salse
Genome Res. November 2010 20: 1545-1557; Published in Advance September 28, 2010, doi:10.1101/gr.109744.110
...Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution Florent Murat 1 , 4 , Jian-Hong Xu 2 , 4 , Eric Tannier 3 , 4 , Michael Abrouk 1 , Nicolas Guilhot 1 , Caroline...

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