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Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
- Shahmir Naseer,
- Thomas C Clark,
- Bertrand Collet,
- Pooran Dewari,
- Damir Baranasic,
- Daniel J Macqueen,
- Pierre Boudinot,
- and Samuel A.M. Martin
Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
...such as histone acetylation and methylation contribute to 48 this regulation by altering DNA accessibility at enhancers and promoters (Mostafavi et al., 49 2016; Kan et al., 2022). Transposase-accessible chromatin with sequencing (ATAC-seq) 50 and chromatin immunoprecipitation and sequencing (ChIP-seq) are widely...
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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
...with phenotypes such as B acute lymphoblastic leukemia (P = 1.8 × 10−91 after FDR), hepatocellular carcinoma (P < 3.4 × 10−39 after FDR), and Helicobacter pylori infection (P = 5.4 × 10−38 after FDR). This finding aligns with earlier studies showing that increased DNA methylation variability frequently occurs...
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Research: An iPSC-based model of 47,XYY Jacobs syndrome reveals a DNA methylation-independent transcriptional dysregulation shared with male X aneuploid cells
- Veronica Astro,
- Kelly Yojanna Cardona-Londoño,
- Lorena Viridiana Cortés-Medina,
- Rawan Alghamdi,
- Gustavo Ramírez-Calderón,
- Fotios Kefalas,
- Jair Dilmé-Capó,
- Santiago Radío,
- and Antonio Adamo
Genome Res. July 2025 35: 1503-1517; Published in Advance June 10, 2025, doi:10.1101/gr.279716.124
...convergence underscores potential commonalities in the molecular pathways underpinning the pathophysiology of male sex-chromosome aneuploidies. Finally, through -wide DNA methylation profiling of JS iPSCs, we demonstrate that a supernumerary Y Chromosome only minimally impacts the methylation status of 47,XYY...
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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...epigenetic information into DNA molecules, enabling LRS to simultaneously map chromatin accessibility, protein binding, and DNA modifications at single-molecule resolution. Such detailed mapping of regulatory landscapes is essential for identifying the mechanisms underlying complex traits and diseases...
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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
.../or record transcriptional activity of their underlying genetic sequences (Bird 2007). One such modification is cytosine DNA methylation (mC), the covalent bond of a methyl group (–CH3) to the fifth carbon of cytosine bases. In plants, mC can occur in three DNA sequence contexts: CG, CHG, and CHH (H = A, C...
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Resource: A systems view on DNA damage response kinetics in Tetrahymena
- Emily Nischwitz,
- Vivien Schoonenberg,
- Rachel Mullner,
- Albert Fradera-Sola,
- Susanne Zimbelmann,
- Joshua J Smith,
- and Falk Butter
Genome Res. January 28, 2026 gr.281000.125; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
...of DNA damage response 36 factors and pathways is critical (Ciccia and Elledge 2010). DNA repair activity is essential in 37 all living organisms, and the dysregulation of any repair pathway has been correlated with 38 disease (Kovalchuk 2016; Jackson and Bartek 2009). 39 The DNA damage response (DDR...
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Method: Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes
- Rachel M. Petersen,
- Christopher M. Vockley,
- and Amanda J. Lea
Genome Res. August 2025 35: 1781-1793; Published in Advance July 14, 2025, doi:10.1101/gr.279957.124
...in direction or magnitude between methylated and unmethylated states. Sites exhibiting methylation-dependent genetic effects are enriched for GWAS and EWAS annotations, implicating them in human disease. Compared with data sets that assay DNA from a single European ancestry individual, our multiplexed assay...
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Research: Assessing DNA methylation detection for primary human tissue using Nanopore sequencing
- Rylee Genner,
- Stuart Akeson,
- Melissa Meredith,
- Pilar Alvarez Jerez,
- Laksh Malik,
- Breeana Baker,
- Abigail Miano-Burkhardt,
- CARD-long-read Team,
- Benedict Paten,
- Kimberley J. Billingsley,
- Cornelis Blauwendraat,
- and Miten Jain
Genome Res. April 2025 35: 632-643; Published in Advance March 7, 2025, doi:10.1101/gr.279159.124
...contributed equally to this work. Corresponding authors: mi.jain@northeastern.edu,kimberley.billingsley@nih.gov, cornelis.blauwendraat@nih.govAbstractDNA methylation most commonly occurs as 5-methylcytosine (5mC) in the human and has been associated with human diseases. Recent developments in single...
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Research: Aberrant homeodomain–DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models
- Yiqiao Zheng,
- Gary D. Stormo,
- and Shiming Chen
Genome Res. February 2025 35: 242-256; Published in Advance December 23, 2024, doi:10.1101/gr.279340.124
...Aberrant homeodomain–DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models Yiqiao Zheng1,2,5, Gary D. Stormo3 and Shiming Chen2,4 1Molecular Genetics and Genomics Graduate Program, Division of Biology & Biomedical Sciences, Washington...
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Research: Nucleosome repositioning in chronic lymphocytic leukemia
- Kristan V. Piroeva,
- Charlotte McDonald,
- Charalampos Xanthopoulos,
- Chelsea Fox,
- Christopher T. Clarkson,
- Jan-Philipp Mallm,
- Yevhen Vainshtein,
- Luminita Ruje,
- Lara C. Klett,
- Stephan Stilgenbauer,
- Daniel Mertens,
- Efterpi Kostareli,
- Karsten Rippe,
- and Vladimir B. Teif
Genome Res. October 2023 33: 1649-1661; Published in Advance September 12, 2023, doi:10.1101/gr.277298.122
...on cell-free DNA to stratify patients and monitor disease progression.Chronic lymphocytic leukemia (CLL) is the most common blood cancer in adults in the Western world. Over the past decade, novel therapies against specific targets, like Bruton tyrosine kinase, have emerged in parallel with an increased...
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