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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
...function. Mutations are analyzed using paralogs grouped into functional families with highly similar functions, identifying 355 functional impact events (FIEs) through their proximity and clustering near to functional sites. The use of functional family paralogs to map mutations to protein structures from...
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Research: Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles
- Xuejing Wang and
- Gerald Heckel
Genome Res. June 2024 34: 851-862; Published in Advance July 2, 2024, doi:10.1101/gr.278487.123
...) Positively selected regions of continental voles had low Δπ, ΔTajima's D, and ΔAF. Genes belonging to the epoxygenase P450 pathway on M. arvalis Chromosome 4 are marked with green. (B) In Orkney voles, Δπ, ΔTajima's D, and ΔAF of positively selected regions did not form clusters outstanding from the genomic...
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Research: Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza
- Rodolphe Dombey,
- Daniel Buendía-Ávila,
- Verónica Barragán-Borrero,
- Laura Diezma-Navas,
- Arturo Ponce-Mañe,
- José Mario Vargas-Guerrero,
- Rana Elias,
- and Arturo Marí-Ordóñez
Genome Res. March 2025 35: 522-544; Published in Advance March 4, 2025, doi:10.1101/gr.279532.124
...) and Spirodela (gray). (E) Relative (%) occupancy of each of the TE clusters defined in B and C in Arabidopsis (gray) and Spirodela (colored). (F) Genome browser capture of the distribution of H3K9me1 and H3K9me2 enrichments, together with DNA methylation, along genes and transposons in Spirodela. (G) Venn...
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Research: Convergent relaxation of molecular constraint in herbivores reveals the changing role of liver and kidney functions across mammalian diets
- Matthew D. Pollard,
- Wynn K. Meyer,
- and Emily E. Puckett
Genome Res. December 2024 34: 2176-2189; Published in Advance November 22, 2024, doi:10.1101/gr.278930.124
..., PNLIPRP1, has convergently lost function in multiple herbivorous mammals, suggesting a relaxation of selective constraint in herbivores compared to carnivores (Hecker et al. 2019). The protein encoded by this gene, PL-RP1, shows little to no detectable lipase activity and instead acts as a competitive...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
..., a particular gene of interest (GOI) remains a persistent experimental and conceptual challenge. This gene-centric question is complicated by the multilayered regulatory environment in which each gene resides, comprising 3D chromatin structure, enhancer–promoter looping, DNA accessibility, histone modifications...
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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
...transposable element (TE) activity in the animal germline via a specialized class of small RNAs called piwi-interacting RNAs (piRNAs). piRNAs are produced from discrete genomic regions called piRNA clusters (piCs). Although the molecular processes by which piCs function are relatively well understood...
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Method: Unveiling the functional fate of duplicated genes through expression profiling and structural analysis
- Alex Warwick Vesztrocy,
- Natasha Glover,
- Paul D. Thomas,
- Christophe Dessimoz,
- and Irene Julca
Genome Res. October 2025 35: 2273-2284; Published in Advance August 14, 2025, doi:10.1101/gr.280166.124
...of evolution (family-specific factors) for each gene tree (Fig. 1A). A factor greater than one indicates that a gene family is evolving more rapidly than average, potentially reflecting relaxed functional constraints, whereas a factor below one suggests slower evolution, which may reflect stronger functional...
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Mini-Review: Revisiting models of enhancer–promoter communication in gene regulation
- Gilad Barshad and
- Charles G. Danko
Genome Res. June 2025 35: 1277-1286; doi:10.1101/gr.278389.123
...: the structural bridge model, in which enhancers and promoters come into close proximity through stable, protein-mediated interactions, and the hub model, in which dynamic clusters of transcription-associated proteins facilitate communication over variable distances. Emerging evidence suggests that although...
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Method: Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease
- Tanner D. Jensen,
- Bohan Ni,
- Chloe M. Reuter,
- John E. Gorzynski,
- Sarah Fazal,
- Devon Bonner,
- Rachel A. Ungar,
- Pagé C. Goddard,
- Archana Raja,
- Euan A. Ashley,
- Jonathan A. Bernstein,
- Stephan Zuchner,
- Undiagnosed Diseases Network,
- Michael D. Greicius,
- Stephen B. Montgomery,
- Michael C. Schatz,
- Matthew T. Wheeler,
- and Alexis Battle
Genome Res. April 2025 35: 914-928; Published in Advance March 20, 2025, doi:10.1101/gr.279323.124
...to predict SVs under selection constraints but not regulatory SVs, and all tools have limited capability in finding functional SVs that modulate gene expression. In addition to SVs, variation at tandem repeat loci contributes to gene expression differences (Gymrek et al. 2016; Bakhtiari et al. 2021). Repeat...
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Research: Genome-wide patterns of selection–drift variation strongly associate with organismal traits across the green plant lineage
- Kavitha Uthanumallian,
- Andrea Del Cortona,
- Susana M. Coelho,
- Olivier De Clerck,
- Sebastian Duchene,
- and Heroen Verbruggen
Genome Res. August 2024 34: 1130-1139; Published in Advance August 29, 2024, doi:10.1101/gr.279002.124
...ancestors from which a large diversity of land plants has evolved (Wang et al. 2020). Green algae feature a broad range of structural complexity, from unicellular and colonial algae to various more complex body architectures in the green seaweeds and land plants. We will use the term “body architecture...
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