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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
...me2 but high DNA methylation (except state 20, which is enriched in transcriptional start sites), corresponding to >80% of SUVH1 and SUVH3-binding sites; states 14 and 15 (5034 loci; 7.8% of the ), long TEs enriched in DNA methylation and H3K9me2, contributing to 25% of MBD5 and MBD6 targets, which...
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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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Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
- David R. Lougheed,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
...: a program to analyze DNA sequences. Nucleic Acids Res 27: 573–580. doi:10.1093/nar/27.2.573 ↵Blauw HM, van Rheenen W, Koppers M, Van Damme P, Waibel S, Lemmens R, van Vught PWJ, Meyer T, Schulte C, Gasser T, et al. 2012. NIPA1 polyalanine repeat expansions are associated with amyotrophic lateral sclerosis...
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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
.... Identification of rare de novo epigenetic variations in congenital disorders. Nat Commun 9: 2064. doi:10.1038/s41467-018-04540-x ↵Bird AP. 1986. CpG-rich islands and the function of DNA methylation. Nature 321: 209–213. doi:10.1038/321209a0 ↵Caylor RC. 2023. Nonrandom X chromosome inactivation detection. Curr...
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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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Method: High-fidelity bidirectional translation between single-cell transcriptomes and DNA methylomes with scBOND
- Kehan Lang,
- Chenyang Jia,
- Siyu Li,
- Yi Guo,
- Dingjun Hu,
- and Shengquan Chen
Genome Res. March 26, 2026 ; Published in Advance March 26, 2026, doi:10.1101/gr.281350.125
..., these algorithms are challenging to apply for cross-modality translation between scRNAseq and scDNAm data. This is because of the unique challenges presented by scDNAm data, including its lower coverage, continuous numerical nature (with DNA methylation levels ranging between zero and one), and the complex...
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Research: Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries
- Shaoqiang Hu,
- Xiangguo Zeng,
- Yuguo Liu,
- Yongping Li,
- Minghao Qu,
- Wen-Biao Jiao,
- Yongchao Han,
- and Chunying Kang
Genome Res. October 2024 34: 1582-1594; Published in Advance October 15, 2024, doi:10.1101/gr.279378.124
...the tissue culture process of cultivated strawberry to reveal features of somaclonal variation. DNA mutation and methylation changes were analyzed at single base resolution in regenerated plants obtained at two hormone levels and two culture times. We chose the strawberry cultivar “Beni hoppe” to assemble...
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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
...and stochastic accumulation of epigenetic changes, such as DNA methylation variability, with advancing age. Although increasingly recognized for its potential role in aging biology, its extent, biological significance, and population specificity remain insufficiently characterized. Here, we present the first...
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Method: EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
- Shuyu Zhang,
- Quan Zou,
- Mengting Niu,
- Zhibin Lv,
- Antony Stalin,
- and Ximei Luo
Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
...combinations, which provides experimental evidence for species-adaptive encoding strategies.DNA methylation is a form of DNA epigenetic modification, which modulates the genetic performance without changing the DNA sequence (Moore et al. 2013). Numerous studies have shown that DNA methylation can alter...
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Research: Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation
- Alejandro Martin-Trujillo,
- Paras Garg,
- Nihir Patel,
- Bharati Jadhav,
- and Andrew J. Sharp
Genome Res. February 2023 33: 184-196; Published in Advance December 28, 2022, doi:10.1101/gr.277057.122
...of quantitative trait loci (QTLs) often allows characterization of the functional consequences of sequence variation on gene expression (eQTLs) (Dixon et al. 2007; Göring et al. 2007; Stranger et al. 2007), DNA methylation (mQTLs) (Martin-Trujillo et al. 2020; Villicaña and Bell 2021), histone modifications (Mc...

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