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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
...and methylome analyses in oocytes revealed that DNA methylation is primarily restricted to transcribed regions (Kobayashi et al. 2012). These transcription events reshape the histone methylation landscape, guiding the DNMT complex to specific genomic regions. Specifically, the transcription-coupled loss of H3K4...
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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
...the entire X Chromosome with long reads measuring the level of methylation and genomic variants to gain allele-specific information (Fig. 2E; Lee et al. 2020). This provides a far more quantitative and comprehensive view than targeting a few genes (Johansson et al. 2023), enabling investigation of severely...
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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
...implicating environmental exposures. Infectious agents, such as cytomegalovirus, have also been shown to induce widespread methylation variance in a cell composition-independent manner (Bergstedt et al. 2022). At the chromatin level, drift-CpGs are enriched in repressive Polycomb-bound regions (Slieker et al...
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Resource: A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq
- Sophia C. Gaynor-Gillett,
- Lijun Cheng,
- Manman Shi,
- Jason Liu,
- Gaoyuan Wang,
- Megan Spector,
- Qiuyu Guo,
- Le Qi,
- Mary Flaherty,
- Martha Wall,
- Ahyeon Hwang,
- Mengting Gu,
- Zhanlin Chen,
- Yuhang Chen,
- PsychENCODE Consortium,
- Jennifer R. Moran,
- Jing Zhang,
- Donghoon Lee,
- Mark Gerstein,
- Daniel Geschwind,
- and Kevin P. White
Genome Res. August 2025 35: 1887-1901; Published in Advance July 11, 2025, doi:10.1101/gr.279584.124
...equally to this work. Corresponding author: sgillett@cornellcollege.eduAbstractGenome-wide association studies (GWASs) and expression analyses implicate noncoding regulatory regions as harboring risk factors for psychiatric disease, but functional characterization of these regions remains limited. Here...
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Research: Adaptation of centromeres to breakage through local genomic and epigenomic remodeling in wheat
- Jingwei Zhou,
- Yuhong Huang,
- Huan Ma,
- Yiqian Chen,
- Chuanye Chen,
- Fangpu Han,
- and Handong Su
Genome Res. November 2025 35: 2461-2471; Published in Advance September 30, 2025, doi:10.1101/gr.280913.125
...in the centromeric regions of Dt1BS (left), Dt6BS (middle), and Dt7AS (right), compared to their corresponding regions in CS wheat. Neocentromeres and their syntenic positions in CS are highlighted in gray. IGV snapshot showing DNA methylation levels (CG, CHG, and CHH contexts), gene annotations, and genomic...
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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
...of identifying methylation-dependent regulatory activity at many thousands of genomic regions simultaneously and allows for the testing of causal relationships between DNA methylation and gene expression on a region-by-region basis. Here, we develop a multiplexed mSTARR-seq protocol to assay naturally occurring...
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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
...(RdDM targets) that are highly enriched in non-CG methylation. Furthermore, these results suggest that the binding of different combinations of mC readers to a single genomic site may form its own code that might define or represent the epigenomic context of the region.Assessing the effects...
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Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
- Medhat Mahmoud,
- Daniel P. Agustinho,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
...assessment of genomic and epigenomic changes within complex regions (Logsdon et al. 2020; Mahmoud et al. 2021; Vollger et al. 2025). Nevertheless, long-read sequencing requires specialized analysis techniques to unlock its full potential, often requiring in-depth knowledge of rapidly evolving bioinformatic...
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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
...G methylation, potentially ascribable to the nonclonal nature of this cell population (Supplemental Fig. S18C; Wagner et al. 2014). On the other hand, methylated CpGs in clonal iPSC lines are significantly more homogenous (Supplemental Fig. S18D). Finally, we analyzed the differentially methylated regions (DMRs...
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Research: Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts
- Yanis Zekri,
- Sebastian Gregoricchio,
- Elif Yapıcı,
- Chia-Chi Flora Huang,
- Tunç Morova,
- Umut Berkay Altıntaş,
- Gozde Korkmaz,
- Nathan A. Lack,
- and Wilbert Zwart
Genome Res. July 2025 35: 1530-1543; Published in Advance June 10, 2025, doi:10.1101/gr.280320.124
...). Although informative, they are not quantitative, incapable of determining direct enhancer activity, and cannot uncouple epigenomic from genomic mechanisms. On the other hand, reporter assays overcome some of these limitations by measuring enhancer activity on nonchromatinized DNA templates, isolating...

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