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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
...”) number and subsequent divergence of function (Hahn 2009).Approximately 75% of lung cancers have WGD events during their evolutionary history (Jamal-Hanjani et al. 2017). Furthermore, changes in gene copy number owing to aneuploidy, in which chromosomes or chromosomal regions are gained or lost, represent...
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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...-expressing), and an unidentified wb-expressing somatic lineage (Fig. 1C; Supplemental Fig. S1H; Supplemental Table S1; Kuhn et al. 1991; Kelly et al. 2002). For this study, we focus on the GSC-like and CySC-like clusters.The GSC-like and CySC-like clusters followed expected gene expression patterns for known cell-type- and stage...
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Research: Distinct classes of lamina-associated domains are defined by differential patterns of repressive histone methylation
- Caden J. Martin,
- Elizabeth A. Oser,
- Prabakaran Nagarajan,
- Liudmila V. Popova,
- Benjamin D. Sunkel,
- Benjamin Z. Stanton,
- and Mark R. Parthun
Genome Res. September 2025 35: 1959-1974; Published in Advance August 5, 2025, doi:10.1101/gr.280380.124
...3K27me3, H3K14ac, H3K27ac, and H3K9ac in MEF cell lines derived from the same mouse colony, and cluster LADs based on the abundance and distribution of these features across LADs. We find that LADs fall into three groups, each enriched in a unique set of histone modifications and genomic features...
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Research: The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution
- Xinghua Li,
- Judith E. Mank,
- and Liping Ban
Genome Res. July 2024 34: 997-1007; Published in Advance August 5, 2024, doi:10.1101/gr.278794.123
...:10.1038/nbt.2727 ↵Cabrero J, López-León MD, Teruel M, Camacho JPM. 2009. Chromosome mapping of H3 and H4 histone gene clusters in 35 species of acridid grasshoppers. Chromosome Res 17: 397–404. doi:10.1007/s10577-009-9030-5 ↵Cantalapiedra CP, Hernández-Plaza A, Letunic I, Bork P, Huerta-Cepas J. 2021...
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Research: The chromatin landscape of the histone-possessing Bacteriovorax bacteria
- Georgi K. Marinov,
- Benjamin Doughty,
- Anshul Kundaje,
- and William J. Greenleaf
Genome Res. January 2025 35: 109-123; Published in Advance November 21, 2024, doi:10.1101/gr.279418.124
...) on the other. These observations also contrast with those from ATAC-seq for C. crescentus, which does not possess histones and in whose ribosomal RNA clusters were reported to be one of a handful of highly transposase-inaccessible transcribed regions (HINTs) (Melfi et al. 2021).Other genes in which...
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Method: Parallel analysis of replication timing, gene expression, and copy number with PARTAGE
- Lakshana Sruthi Sadu Murari,
- Quinn Dickinson,
- Silvia Meyer-Nava,
- and Juan Carlos Rivera-Mulia
Genome Res. April 2026 36: 802-813; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
...and with ≥4× Δ log2TPM were considered. (E) Reactome ontology analysis of the major cluster (blue) is shown. (F) Exemplary chromosome regions harboring variable genes that are induced during cell cycle progression (CDK1, TOP2A, and CCNB1).PARTAGE also enables the profiling of cell cycle phase...
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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: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
..., and SUVH3 exhibited preferential localization to heterochromatic peri-centromeric regions, whereas the other MBD proteins studied were mostly localized along euchromatic chromosome arms (Fig. 2B). MBD1, MBD2, and MBD4 were mostly associated with genes, whereas MBD5, MBD6, SUVH1, and SUVH3 were primarily...
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Method: Characterization of meiotic recombination intermediates through gene knockouts in founder hybrid mice
- Benjamin Davies,
- Gang Zhang,
- Daniela Moralli,
- Samy Alghadban,
- Daniel Biggs,
- Chris Preece,
- Peter Donnelly,
- and Anjali Gupta Hinch
Genome Res. November 2023 33: 2018-2027; Published in Advance November 17, 2023, doi:10.1101/gr.278024.123
...coordinate descent. J Stat Softw 33: 1–22. doi:10.18637/jss.v033.i01 ↵Gergelits V, Parvanov E, Simecek P, Forejt J. 2021. Chromosome-wide characterization of meiotic noncrossovers (gene conversions) in mouse hybrids. Genetics 217: 1–14. doi:10.1093/genetics/iyaa013 ↵Gregorova S, Gergelits V, Chvatalova I...
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Research: Variation in histone configurations correlates with gene expression across nine inbred strains of mice
- Anna L Tyler,
- Catrina Spruce,
- Romy Kursawe,
- Annat Haber,
- Robyn L Ball,
- Wendy A Pitman,
- Alexander D Fine,
- Narayanan Raghupathy,
- Michael Walker,
- Vivek M Philip,
- Christopher L Baker,
- J. Matthew Mahoney,
- Gary A. Churchill,
- Jennifer J Trowbridge,
- Michael L Stitzel,
- Kenneth Paigen,
- Petko M Petkov,
- and Gregory W Carter
Genome Res. May 22, 2023 gr.277467.122; Published in Advance May 22, 2023, doi:10.1101/gr.277467.122
...genetic regulation of both modalities. This is seen as a87 clustering of individuals from the same strain in principal component plots of transcriptomic and88 epigenetic features (Fig. 1). Patterns of gene expression (Fig. 1A), DNA methylation (Fig. 1B)89 and individual histone modifications (Fig. 1C...
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