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Research: Epigenetic and evolutionary features of ape subterminal heterochromatin
- DongAhn Yoo,
- Katherine M. Munson,
- and Evan E. Eichler
Genome Res. January 2026 36: 38-49; Published in Advance October 22, 2025, doi:10.1101/gr.280987.125
...insertions and lineage-specific duplicated genes. Our findings suggest independent evolution of subterminal caps converging on a common genetic and epigenetic structure that promoted ectopic exchange as well as the emergence of novel genes at transition regions between euchromatin and heterochromatin...
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Research: Dynamic A-to-I RNA editing in response to gut microbiome in honey bees
- Yuange Duan,
- Min Huang,
- Lin Ye,
- Ling Ma,
- Yashuai Wu,
- Yating Du,
- Jiyao Liu,
- Fan Song,
- Li Tian,
- Wanzhi Cai,
- Hu Li,
- Xin Zhou,
- and Shiqi Luo
Genome Res. March 4, 2026 gr.280291.124; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
...Dynamic A-to-I RNA editing in response to gut microbiome 1 in honey bees 2 3 Yuange Duan1 #, Min Huang1 #, Lin Ye1 #, Ling Ma1, Yashuai Wu1, Yating Du1, Jiyao Liu1, 4 Fan Song1, Li Tian1, Wanzhi Cai1, Hu Li1, Xin Zhou1, Shiqi Luo1 * 5 6 1. State Key Laboratory of Agricultural and Forestry...
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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
...of Oncobiology and Epigenetics, University of Lodz, 90-237 Lodz, Poland ↵6 These authors contributed equally to this work. Corresponding authors: urszula.mcclurg@liverpool.ac.uk, mratajewski@cbm.pan.pl, lpulaski@uni.lodz.plAbstractTranscriptional regulation lies at the heart of cellular identity and function...
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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
...authors: watersto@uw.edu, valerie.reinke@yale.eduAbstractA catalog of transcription factor (TF) binding sites in the is critical for deciphering regulatory relationships. Here, we present the culmination of the efforts of the modENCODE (model organism Encyclopedia of DNA Elements) and modERN (model...
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Method: Polyomino reconstructs spatial transcriptomic profiles with single-cell resolution via a region-allocation method
- Quanyou Cai,
- Lihui Lin,
- Xin Liu,
- and Jiekai Chen
Genome Res. November 2025 35: 2513-2526; Published in Advance October 22, 2025, doi:10.1101/gr.280532.125
...directly within the spatial context, such as clustering, pseudotime analysis, and spatial neighborhood modeling. Such capability enables more precise characterization of spatial heterogeneity and cellular interactions.ResultsThe Polyomino algorithmPolyomino begins by creating square (or hexagon) bins...
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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...-based transcriptional regulatory networks. Overall, these results illustrate the power of an approach combining genetic perturbation with high-resolution epigenomic profiling; the latter enables a close examination of the interplay between TFs and nucleosomes -wide, providing a deeper, more mechanistic understanding...
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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
...considered significantly associated with seasonal stage. Expression profiles of these significant genes were then clustered to explore temporal dynamics using DEGreport (v1.44) (https://bioconductor.org/packages/DEGreport). As these genes had already been filtered for statistical significance and lacked...
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Research: Transcription and potential functions of a novel XIST isoform in male peripheral glia
- Kevin S. O'Leary,
- Meng-Yen Li,
- Kevyn Jackson,
- Lijie Shi,
- Elena Ezhkova,
- Bernice E. Morrow,
- and Deyou Zheng
Genome Res. February 2026 36: 257-274; Published in Advance December 12, 2025, doi:10.1101/gr.280832.125
...integrated analyses of single-cell RNA-seq data from multiple human tissues and organs. Single-cell epigenomic data further indicate that the expression is likely driven by an alternative promoter at the end of the first exon, resulting in at least one shorter transcript (referred to as sXIST) that is active...
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Research: Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing
- Keegan S. Krick,
- Marissa Maroni,
- Erica Korb,
- Kristen W. Lynch,
- and Elizabeth A. Heller
Genome Res. June 2025 35: 1301-1312; Published in Advance April 24, 2025, doi:10.1101/gr.280082.124
...samples clustered much more strongly by data set when considering transcript abundance. This analysis highlighted a general convergence at the level of exon inclusion, with KCl-stimulated samples looking more similar to one another despite origin, whereas sample heterogeneity was driven largely by data...
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Research: Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations
- Xiu Fan,
- Qili Qian,
- Wenran Li,
- Tianzi Liu,
- Changqing Zeng,
- Peilin Jia,
- Huandong Lin,
- Xin Gao,
- Li Jin,
- Mingfeng Xia,
- Sijia Wang,
- and Fan Liu
Genome Res. October 2025 35: 2173-2188; Published in Advance August 1, 2025, doi:10.1101/gr.280155.124
...decreased variability (negative drift). Integration with single-cell RNA-seq data demonstrates that positive drift-CpGs are associated with increased transcriptional variability and upregulation in specific cell types, whereas negative drift-CpGs exhibit the opposite effect. We develop epigenetic drift...
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