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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
...allele-specific gene expression across large imprinted domains. In this review, we highlight the features that define ICRs as a distinct class of cis-regulatory regions, from their ability to maintain germline-inherited DNA methylation to their multifunctional roles in transcriptional control. For each...
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Method: Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation
- Sophia N. Lee,
- Erin C. Banda,
- Lu Qiao,
- Sarah L. Thompson,
- Karan Singh,
- Ryan A. Hagenson,
- Teresa Davoli,
- Stefan F. Pinter,
- and Jason M. Sheltzer
Genome Res. March 2026 36: 547-560; Published in Advance January 12, 2026, doi:10.1101/gr.280425.125
...of Chromosome 8 and restore euploidy in cells derived from an individual with a complex rearrangement of Chromosome 8p. Transcriptomic analysis revealed 361 differentially expressed genes between the proband and the euploid revertant, highlighting genes both within and outside the 8p region that may contribute...
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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
....Cytosine methylation plays a critical role in genomic imprinting, gene regulation, X-Chromosome inactivation (XCI), cellular differentiation, aging, and tumorigenesis. Cells have an extensive system of proteins that establish these methylation patterns through de novo methylation or demethylation, copy methylation...
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Research: Genetic, epigenetic, and environmental mechanisms govern allele-specific gene expression
- Celine L. St. Pierre,
- Juan F. Macias-Velasco,
- Jessica P. Wayhart,
- Li Yin,
- Clay F. Semenkovich,
- and Heather A. Lawson
Genome Res. June 2022 32: 1042-1057; Published in Advance May 2, 2022, doi:10.1101/gr.276193.121
...-of-origin-dependent ASE in which one parent's allele is silenced via selective epigenetic marks, such as DNA methylation and histone modifications (Umlauf et al. 2004; Barlow and Bartolomei 2014; Inoue et al. 2017). Known imprinted genes compose ∼1% of the human and mouse s, yet play important roles in development...
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Research: Incomplete erasure of histone marks during epigenetic reprogramming in medaka early development
- Hiroto S. Fukushima,
- Hiroyuki Takeda,
- and Ryohei Nakamura
Genome Res. April 2023 33: 572-586; Published in Advance April 28, 2023, doi:10.1101/gr.277577.122
...analyzed histone modification dynamics during epigenetic reprogramming in Japanese killifish, medaka (Oryzias latipes) embryos. Our data revealed that H3K27ac, H3K27me3, and H3K9me3 escape complete reprogramming, whereas H3K4 methylation is completely erased during cleavage stage. Furthermore, we...
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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
...-base resolution methylation levels for individual CpG sites across the . These resources also annotate hypomethylated regions commonly linked to gene promoters, as well as allele-specific methylation patterns relevant to genomic imprinting. Notable examples include MethBase (Song et al. 2013), MethBank (Zhang et...
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Research: The aberrant epigenome of DNMT3B-mutated ICF1 patient iPSCs is amenable to correction, with the exception of a subset of regions with H3K4me3- and/or CTCF-based epigenetic memory
- Varsha Poondi Krishnan,
- Barbara Morone,
- Shir Toubiana,
- Monika Krzak,
- Salvatore Fioriniello,
- Floriana Della Ragione,
- Maria Strazzullo,
- Claudia Angelini,
- Sara Selig,
- and Maria R. Matarazzo
Genome Res. February 2023 33: 169-183; Published in Advance February 24, 2023, doi:10.1101/gr.276986.122
...responsible for the aberrant gene expression pattern and the cellular and developmental defects typical of ICF syndrome. DNA methylation and transcriptional studies of ICF1 patient whole blood and lymphoblastoid cell lines (LCLs) identified several key alterations in epigenetic and gene expression profiles...
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Method: Long-read RNA sequencing reveals allele-specific N⁶-methyladenosine modifications
- Dayea Park and
- Can Cenik
Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
...as only one allele is expressed. Allele-specific DNA methylation and chromatin composition are two well-established epigenetic systems that control imprinted gene expression (Fournier et al. 2002; Singh et al. 2010; Prendergast et al. 2012).ASE can reflect differential rates of transcription, m...
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Research: Positive selective sweeps of epigenetic mutations regulating specialized metabolites in plants
- Kazumasa Shirai,
- Mitsuhiko P. Sato,
- Ranko Nishi,
- Masahide Seki,
- Yutaka Suzuki,
- and Kousuke Hanada
Genome Res. June 2021 31: 1060-1068; Published in Advance May 18, 2021, doi:10.1101/gr.271726.120
...the A. thaliana accessions, differentially methylated regions are concentrated in genes related to specialized metabolites (Kawakatsu et al. 2016). DNA methylation in the promoter region of a gene may alter the production of specialized metabolites in A. thaliana (Kooke et al. 2019). Thus, specialized...
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Research: Epigenetic mapping of the Arabidopsis metabolome reveals mediators of the epigenotype-phenotype map
- Rik Kooke,
- Lionel Morgado,
- Frank Becker,
- Henriëtte van Eekelen,
- Rashmi Hazarika,
- Qunfeng Zheng,
- Ric C.H. de Vos,
- Frank Johannes,
- and Joost J.B. Keurentjes
Genome Res. January 2019 29: 96-106; Published in Advance November 30, 2018, doi:10.1101/gr.232371.117
...RILs) in Arabidopsis were especially designed to study the impact of heritable epigenetic variation on complex traits (Johannes et al. 2009), and epigenetic QTL mapping approaches have shown that specific differentially methylated regions (DMRs) in the epiRILs can affect complex traits (Cortijo et al. 2014; Kooke et...
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