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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: 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
..., demonstrating an unprecedented putative cis-regulatory role of Helitrons in Drosophila. Differential expression analysis between species with different preferred hosts reveals divergence in gene expression in heads and larvae. Although TEs’ presence does not affect overall gene expression, we observe 6...
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Research: Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus
- Rita Tam,
- Mareike Möller,
- Runpeng Luo,
- Zhenyan Luo,
- Ashley Jones,
- Sambasivam Periyannan,
- John P. Rathjen,
- and Benjamin Schwessinger
Genome Res. June 2025 35: 1364-1376; Published in Advance April 11, 2025, doi:10.1101/gr.280359.124
...of allelic information facilitates robust assessment of allele-specific expression (ASE) uncovering the underlying variations in cis-regulatory elements and epigenetic regulation, which can have important implications on phenotypic variability, as well established in mammals and plants (e.g., Shao et al...
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Research: KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution
- Kai Otsuka,
- Akihiko Sakashita,
- So Maezawa,
- Richard M. Schultz,
- and Satoshi H. Namekawa
Genome Res. March 2025 35: 417-431; Published in Advance March 12, 2025, doi:10.1101/gr.279924.124
...KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and evolution Kai Otsuka1,2, Akihiko Sakashita3,4, So Maezawa2, Richard M. Schultz1,5 and Satoshi H. Namekawa1,3 1Department of Microbiology and Molecular Genetics, University of California, Davis...
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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
...to seven clades of recently duplicated paralogs unique to D. rerio with a minimum of 10 members (for details, see Methods). Using PAML (Yang 2007), we performed likelihood ratio tests to compare two models of evolution for each clade: one in which the genes were evolving under purifying selection, and one...
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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
...suggests that divergence of cis-regulatory regions in nonrecombining regions can cause rapid sex chromosome degeneration and acquisition of dosage compensation simultaneously (Lenormand et al. 2020). Because dosage compensation is thought to evolve during the earlier stages of sex chromosome divergence...
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Research: Comparative epigenomics in distantly related teleost species identifies conserved cis-regulatory nodes active during the vertebrate phylotypic period
- Juan J. Tena,
- Cristina González-Aguilera,
- Ana Fernández-Miñán,
- Javier Vázquez-Marín,
- Helena Parra-Acero,
- Joe W. Cross,
- Peter W.J. Rigby,
- Jaime J. Carvajal,
- Joachim Wittbrodt,
- José L. Gómez-Skarmeta,
- and Juan R. Martínez-Morales
Genome Res. July 2014 24: 1075-1085; Published in Advance April 7, 2014, doi:10.1101/gr.163915.113
...Comparative epigenomics in distantly related teleost species identifies conserved cis -regulatory nodes active during the vertebrate phylotypic period Juan J. Tena 1 , 4 , Cristina González-Aguilera 1 , 4 , Ana Fernández-Miñán 1 , Javier Vázquez...
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Research: Comprehensive isoform-level analysis reveals the contribution of alternative isoforms to venom evolution and repertoire diversity
- Xinhai Ye,
- Chun He,
- Yi Yang,
- Yu H. Sun,
- Shijiao Xiong,
- Kevin C. Chan,
- Yuxuan Si,
- Shan Xiao,
- Xianxin Zhao,
- Haiwei Lin,
- Yang Mei,
- Yufeng Yao,
- Gongyin Ye,
- Fei Wu,
- and Qi Fang
Genome Res. September 2023 33: 1554-1567; Published in Advance October 5, 2023, doi:10.1101/gr.277707.123
...duplication followed by neofunctionalization, gene co-option, and lateral gene transfer are well-established mechanisms driving venom evolution in parasitoid wasps (Martinson et al. 2016, 2017; Huang et al. 2021; Yang et al. 2021; Ye et al. 2022), our understanding of the role of alternative isoforms...
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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
...of cis-regulatory elements. One intrinsic limitation for evolutionary studies is that each enhancer has one ortholog per species barring duplication or deletion, which constrains the sample size for analysis. Within a TE subfamily, each TE is descended from a common ancestor, with each copy evolving...
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Research: Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints
- Manuel Irimia,
- Juan J. Tena,
- Maria S. Alexis,
- Ana Fernandez-Miñan,
- Ignacio Maeso,
- Ozren Bogdanović,
- Elisa de la Calle-Mustienes,
- Scott W. Roy,
- José L. Gómez-Skarmeta,
- and Hunter B. Fraser
Genome Res. December 2012 22: 2356-2367; Published in Advance June 21, 2012, doi:10.1101/gr.139725.112
.... In coregulated gene pairs, each gene of the pair could be reciprocally lost from one of the duplicated regions while keeping the common cis-regulatory elements in both, therefore becoming two nonassociated genes with fully functional regulatory landscapes. In the case of GRBs, the coding sequences of extra...

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