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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
...species.ResultsGenome assemblies and gene annotationTo investigate the potential role of TEs in host shift of cactophilic Drosophila species, we performed Oxford Nanopore Technologies (ONT) long-read sequencing on species that have different preferential cacti as hosts: D. buzzatii (Opuntia sp.), D...
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Review: The superpowers of imprinting control regions
- Bertille Montibus,
- Franck Court,
- and Philippe Arnaud
Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
..., can function as promoters, enhancers, and/or insulators, thereby regulating both proximal and distal target genes in an allele-specific manner.Genomic imprintingIn the mid-1980s, it was observed that fertilized mouse oocytes containing either two maternal or two paternal s failed to develop to term...
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Research: Dynamic metabolic and molecular changes during seasonal shrinking in Sorex araneus
- William R. Thomas,
- Cecilia Baldoni,
- Yuanyuan Zeng,
- David Carlson,
- Julie Holm-Jacobsen,
- Marion Muturi,
- Dominik von Elverfeldt,
- Tue B. Bennike,
- Dina K.N. Dechmann,
- John Nieland,
- Angelique P. Corthals,
- and Liliana M. Dávalos
Genome Res. January 2026 36: 61-70; Published in Advance November 4, 2025, doi:10.1101/gr.280639.125
...is highest in autumn and early winter when snow is too scarce to offer insulation, increasing demand for glucose to prevent starvation. We discovered an upregulation of the gluconeogenesis pathways in winter juveniles (Fig. 4), including the overexpression of aldehyde dehydrogenases (ALDH1B1 and ALDH3A2...
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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
...) and genomic size (∼0.6 Mbp) (Supplemental Fig. S3), TAD border insulation strength (R2 = 0.77–1.00) (Supplemental Fig. S4) and intra-TAD contact frequencies (R2 = 0.91–1.00) (Supplemental Fig. S5), and genomic positions of both TADs (Jaccard index [JI] = 0.76–0.80; called at 50 kb resolution), and sub...
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Research: A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress
- Taylor Anglen,
- Irene M. Kaplow,
- Baekgyu Choi,
- Enya Dewars,
- Robin M. Perelli,
- Kevin T. Hagy,
- Duc Tran,
- Megan E. Ramaker,
- Svati H. Shah,
- Inkyung Jung,
- Andrew P. Landstrom,
- Ravi Karra,
- Yarui Diao,
- and Charles A. Gersbach
Genome Res. November 2025 35: 2418-2432; Published in Advance October 22, 2025, doi:10.1101/gr.280825.125
...University School of Medicine, Durham, North Carolina 27708, USA; 2Center for Advanced Genomic Technologies, Duke University, Durham, North Carolina 27708, USA; 3Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA; 4Department of Biological Science, Korea Advanced...
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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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Resource: Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships
- Michelle Kudron,
- Louis Gevirtzman,
- Alec Victorsen,
- Bridget C. Lear,
- Jiahao Gao,
- Jinrui Xu,
- Swapna Samanta,
- Emily Frink,
- Adri Tran-Pearson,
- Chau Huynh,
- Dionne Vafeados,
- Ann Hammonds,
- William Fisher,
- Martha Wall,
- Greg Wesseling,
- Vanessa Hernandez,
- Zhichun Lin,
- Mary Kasparian,
- Kevin White,
- Ravi Allada,
- Mark Gerstein,
- LaDeana Hillier,
- Susan E. Celniker,
- Valerie Reinke,
- and Robert H. Waterston
Genome Res. December 2024 34: 2319-2334; Published in Advance October 22, 2024, doi:10.1101/gr.279037.124
..., Kevin White12, Ravi Allada4, Mark Gerstein5,6,13, LaDeana Hillier2, Susan E. Celniker9, Valerie Reinke1 and Robert H. Waterston2 1Department of Genetics, Yale University, New Haven, Connecticut 06520, USA; 2Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington...
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Research: Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis
- Olga M. Sigalova,
- Mattia Forneris,
- Frosina Stojanovska,
- Bingqing Zhao,
- Rebecca R. Viales,
- Adam Rabinowitz,
- Fayrouz Hammal,
- Benoît Ballester,
- Judith B. Zaugg,
- and Eileen E.M. Furlong
Genome Res. May 2025 35: 1138-1153; Published in Advance April 15, 2025, doi:10.1101/gr.279652.124
...as the primary source of information. The Drosophila dm6 reference served as the input for the training process. In essence, the Basenji model seeks to generate accurate and high-resolution genomic tracks by learning the complex relationships between DNA sequences and their corresponding genomic profiles (Kelley...
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Method: BINDER achieves accurate identification of hierarchical TADs by comprehensively characterizing consensus TAD boundaries
- Yangyang Liu,
- Bingqiang Liu,
- and Juntao Liu
Genome Res. May 2025 35: 1194-1208; Published in Advance March 17, 2025, doi:10.1101/gr.279647.124
...-throughput technique known as Hi-C, have greatly advanced the development of 3D genomics (Dekker et al. 2002; Dostie et al. 2006; Lieberman-Aiden et al. 2009). For instance, studies by Dixon et al. (2012) demonstrated that chromosomes encompass numerous chromatin domains spanning tens to hundreds of kilobases. Within...
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Research: Genomic context sensitivity of insulator function
- André M. Ribeiro-dos-Santos,
- Megan S. Hogan,
- Raven D. Luther,
- Ran Brosh,
- and Matthew T. Maurano
Genome Res. March 2022 32: 425-436; Published in Advance January 26, 2022, doi:10.1101/gr.276449.121
...is influenced by the binding of insulator proteins such as CTCF, which can act as potent enhancer blockers when interposed between an enhancer and a promoter in a reporter assay. But not all CTCF sites -wide function as insulator elements, depending on cellular and genomic context. To dissect the influence...

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