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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
...that the different patterns of PTM enrichment between the three LAD clusters could affect their three-dimensional organization within the nucleus. We performed 3D DNA FISH to test whether the association with the nuclear lamina varies between clusters, using Lamin A/C staining to visualize the nuclear periphery (Fig...
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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
...author: ryan.lister@uwa.edu.auAbstractIn plants, cytosine DNA methylation (mC) is largely associated with transcriptional repression of transposable elements, but it can also be found in the body of expressed genes, referred to as gene body methylation (gbM). gbM is correlated with ubiquitously expressed...
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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
...to the transcription machinery. As a result, transcription levels can undergo repression leading to a silencing effect of the associated gene. The dominant form of DNA methylation in terminally differentiated human cells occurs proximal to a guanosine residue, and the resulting loci are often referred to as CpG sites...
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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...independent of copy number changes; these processes increase the tumor mutation burden and thus the likelihood of novel driver mutations. Mutations arise through impairments in DNA-damage repair pathways (Wu et al. 2020), endogenous processes including APOBEC mutagenesis, and exogenous factors such as smoking...
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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
...for estimating tumor load and identifying the tissue of origin across a wide range of cancer types (Guo et al. 2017; Moss et al. 2018; Liu et al. 2020). Enrichment strategies like cfMeDIP have been used to focus methylation profiling on cfDNA to establish cancer-specific patterns for early detection...
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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
...6, P7, and P4, respectively (Supplemental Figure 232 S6A). 233 8 Other gene families not directly involved in DNA repair exhibited similar time-dependent 234 transcriptional regulation, but grouped into distinct clusters, displaying divergent expression 235 patterns at the protein level. For example...
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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
...genes with dosage sensitivity to the Y number are shown. Pearson's correlation coefficient (R), P-value, and FDR are indicated.The presence of an extra Y Chromosome results in subtle changes in DNA methylationTo understand the impact of an extra Y Chromosome on global DNA methylation, we performed...
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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
...aging. These include changes in DNA methylation, histone modifications, chromatin remodeling, and noncoding RNAs. Collectively, such alterations disrupt gene regulatory networks, leading to transcriptional dysregulation, loss of cellular homeostasis, and increased vulnerability to age-related diseases...
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Research: A DNA methylation haplotype block landscape in human tissues and preimplantation embryos reveals regulatory elements defined by comethylation patterns
- Yan Feng,
- Zhiqiang Zhang,
- Yuyang Hong,
- Yi Ding,
- Leiqin Liu,
- Siqi Gao,
- Hai Fang,
- and Jiantao Shi
Genome Res. December 2023 33: 2041-2052; Published in Advance November 8, 2023, doi:10.1101/gr.278146.123
....25, 81.5% of CpG sites in MHBs were covered by ATAC-seq peaks, whereas the proportions in UMRs and LMRs were 53% and 60.5%, respectively. This pattern was highly robust across all individual tissue types (Supplemental Fig. S4), suggesting that MHBs represent regulatory elements defined by DNA methylation...
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Research: H3K27 and H3K9 methylation mask potential CTCF binding sites to maintain 3D genome integrity
- Kei Fukuda,
- Chikako Shimura,
- and Yoichi Shinkai
Genome Res. October 2025 35: 2199-2210; Published in Advance August 5, 2025, doi:10.1101/gr.280732.125
..., but there is also a certain degree of cell type specificity, the regulation of which is influenced by transcription factors and epigenomic modifications, such as DNA methylation (Wang et al. 2012; Spracklin et al. 2023; Monteagudo-Sánchez et al. 2024). Recent studies have revealed that SETDB1 and EHMT1/2, which...

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