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Resource: Epigenomics of embryogenesis in turbot
- Oscar Aramburu,
- Belen G Pardo,
- Ada Jimenez-Gonzalez,
- Andrés Blanco-Hortas,
- Daniel Macqueen,
- Carmen Bouza,
- and Paulino Martinez
Genome Res. November 4, 2025 gr.280355.124; Published in Advance November 4, 2025, doi:10.1101/gr.280355.124
...cell. This process is orchestrated by changes 11 in transcriptional regulation, influenced by chromatin accessibility and 12 epigenetic modifications, enabling transcription factor accessibility. Epigenomic 13 regulation of embryogenesis has been studied in model fish, but little attention 14 has been...
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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
...of the cell cycle are collected by fluorescence-activated cell sorting (FACS). Next, genomic DNA and nuclear RNA are copurified using silica-based strategies. Genomic DNA is processed following the optimized Repli-seq method, consisting in enzymatic fragmentation, immunoprecipitation with antibodies against...
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Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M. Riley,
- Randa Elsayed,
- Mark D. Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C. Nelson
Genome Res. April 2026 36: 695-712; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...and to associated organs including the liver and pancreas. We used functional genomic approaches to identify highly conserved endodermal cis-regulatory modules (CRMs) functioning across the 400 million years of evolution separating zebrafish and humans. Our analyses suggest that there are few endoderm-specific CRMs...
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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
...such as compaction and accessibility, whereas endogenous DNA allows for in cellulo analysis under physiological conditions. Similarly, proteins can be purified and studied in vitro, expressed exogenously from a plasmid, or endogenously produced within the cell from genomic DNA. Although plasmid-based expression...
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Method: Statistically rigorous and computationally efficient chromatin stripe detection with Quagga
- Fan Feng,
- Sean Moran,
- Anders S. Hansen,
- Xiaotian Zhang,
- and Jie Liu
Genome Res. January 2026 36: 159-168; Published in Advance November 12, 2025, doi:10.1101/gr.280132.124
...determination. Therefore, integrated analysis of stripes with genomic and epigenomic features at a -wide scale shows vast potential in understanding the cooperation between regulatory elements in 3D nucleome. To this end, we present Quagga, a computational tool for detection and statistical verification...
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Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
- Laura Blanco-Berdugo,
- Alexis Garretson,
- and Beth L. Dumont
Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
.... All statistical analyses were performed in R (v. 4.2.2) and RStudio (v. 4.2.2) (R Core Team 2023).Genomic annotation and epigenomic enrichment of dnSNVsdnSNVs were annotated using SnpEff (v. 5.0) (Cingolani et al. 2012). The intersect command within BEDTools (v. 2.28.0) (Quinlan and Hall 2010...
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Research: Polycomb misregulation in enterocytes drives tissue decline in the aging Drosophila intestine
- Sarah M. Leichter,
- Kami Ahmad,
- and Steven Henikoff
Genome Res. January 2026 36: 102-114; Published in Advance November 17, 2025, doi:10.1101/gr.281058.125
...)–normalized and Z-score-normalized heatmaps from differential analysis of H3K27me3 over genes between 1-day-old cell types. (E–H) UCSC Genome Browser tracks of repressed domains in the three cell types in young guts. (E) The ANTP-C domain is shared between all three cell types. (F–H) A domain encompassing the pi...
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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
...Bertille Montibus, Franck Court and Philippe Arnaud Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, 63000 Clermont-Ferrand, France Corresponding author: philippe.arnaud@uca.frAbstractGenomic imprinting is a specialized mechanism...
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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: 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
...Xiu Fan1,2,10, Qili Qian3,4,10, Wenran Li3,4, Tianzi Liu3,4, Changqing Zeng1,2,5, Peilin Jia1,2, Huandong Lin6, Xin Gao6, Li Jin4,7, Mingfeng Xia6, Sijia Wang3,8 and Fan Liu1,9 1China National Center for Bioinformation, Beijing 100101, China; 2Beijing Institute of Genomics, Chinese Academy...
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