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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...with global developmental delay. They also identified other genetic variations (insertions, SNVs, SVs, duplications, deletions) occurring in cis with proximal regulatory element hypermethylation and predicted to disrupt regulatory element activity.X-Chromosome inactivationAllele-specific methylation...
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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...6BT, United Kingdom; 2Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom; 3Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, United Kingdom; 4University College London Cancer...
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Research: Degrees of convergent evolution in rodent adaptations to arid environments
- Domitille Chalopin,
- Carine Rey,
- Jeremy Ganofsky,
- Juliana Blin,
- Pascale Chevret,
- Marion Mouginot,
- Laurent Guéguen,
- Bastien Boussau,
- Sophie Pantalacci,
- and Marie Sémon
Genome Res. March 2026 36: 472-486; Published in Advance January 21, 2026, doi:10.1101/gr.280089.124
...in the Murinae data set. This convergence in cell proportions very likely shapes the global trend of transcriptome convergence pointed above with PCA and gene modules.Convergent evolution in coding sequences is mosaicStudies on convergent evolution in coding sequences have shown that convergence on the exact...
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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...that gars have lower TE copy numbers and a much lower degree of TE activity than other representative vertebrates (Fig. 3). Together with our inference that gars have the lowest rates of global genomic nucleotide substitution across all vertebrates (Brownstein et al. 2024) and have highly conserved synteny...
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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
...that the branch model does not differentiate among codons, these results reflect a global change in selective pressure across the entire gene in the foreground. Then, we also investigated whether specific sites could be under positive selection with the branch-site model, but we did not observe any significant...
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Method: Pangenome-based genome inference using integer programming
- Ghanshyam Chandra,
- Md Helal Hossen,
- Stephan Scholz,
- Alexander T. Dilthey,
- Daniel Gibney,
- and Chirag Jain
Genome Res. December 2025 35: 2661-2670; Published in Advance August 21, 2025, doi:10.1101/gr.280567.125
...and accessibility of assemblies for global cattle breeds and other bovine species. Genome Biol 24: 139. doi:10.1186/s13059-023-02975-0 ↵Tavakoli N, Gibney D, Aluru S. 2022. Haplotype-aware variant selection for graphs. In Proceedings of the 13th ACM International Conference on Bioinformatics, Computational Biology...
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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
...sequence to associate footprints with specific TFs. The differential binding score is then summarized across individual binding sites to provide a global measure of TF activity. In our case, positive scores indicate higher TF binding in liver, whereas negative scores indicate higher binding in brain...
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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...(Fig. 1E; Supplemental Figs. S21–S23) display expected genomic features in which more gene-poor chromosomes are located more frequently toward the nuclear periphery (Supplemental Figs. S24–S26). Our 3D modeling of all three cell types reveals major differences between 10A cells versus T1 and C1 cells...
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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
..., ASE and methylation differences at locus resolution. Here, we use a long-term asexual clone of the wheat stripe rust fungus Puccinia striiformis f. sp. tritici (Pst) dating back at least 80 years to address these questions in a globally important wheat pathogen (Wellings 2007; Thach et al. 2016...
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Research: Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay
- Bertille Montibus,
- James A. Cain,
- Rocio T. Martinez-Nunez,
- and Rebecca J. Oakey
Genome Res. December 2024 34: 2163-2175; Published in Advance November 22, 2024, doi:10.1101/gr.279430.124
...-specific expression and host isoform regulation in the brain and liver. More globally, host genes were found to exhibit more transcript isoforms than other genes, suggesting an important role for the host/nested genes’ genomic organization in the regulation of transcript diversity. Previous works indicate...
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