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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: Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus
- Rita Tam,
- Mareike Möller,
- Runpeng Luo,
- Zhenyan Luo,
- Ashley Jones,
- Sambasivam Periyannan,
- John P. Rathjen,
- and Benjamin Schwessinger
Genome Res. June 2025 35: 1364-1376; Published in Advance April 11, 2025, doi:10.1101/gr.280359.124
...of allelic information facilitates robust assessment of allele-specific expression (ASE) uncovering the underlying variations in cis-regulatory elements and epigenetic regulation, which can have important implications on phenotypic variability, as well established in mammals and plants (e.g., Shao et al...
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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: Genetic and environmental exposures constrain epigenetic drift over the human life course
- Sonia Shah,
- Allan F. McRae,
- Riccardo E. Marioni,
- Sarah E. Harris,
- Jude Gibson,
- Anjali K. Henders,
- Paul Redmond,
- Simon R. Cox,
- Alison Pattie,
- Janie Corley,
- Lee Murphy,
- Nicholas G. Martin,
- Grant W. Montgomery,
- John M. Starr,
- Naomi R. Wray,
- Ian J. Deary,
- and Peter M. Visscher
Genome Res. November 2014 24: 1725-1733; Published in Advance September 23, 2014, doi:10.1101/gr.176933.114
...of gene expression. DNAm is dynamic, influenced by both environmental and genetic factors. Epigenetic drift is the divergence of the epigenome as a function of age due to stochastic changes in methylation. Here we show that epigenetic drift may be constrained at many CpGs across the human genome by DNA...
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Perspective: The Mendelian disorders of the epigenetic machinery
- Hans Tomas Bjornsson
Genome Res. October 2015 25: 1473-1481; doi:10.1101/gr.190629.115
....0/. Perspective 25:1473–1481 Published by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/15; www..org Genome Research 1473 www..org of epigenetic gene disorders (Berdasco and Esteller 2013; Kleefstra et al. 2014), here I have included only genes with known epigenetic domains that fulfill criteria as one...
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Research: Fixation of allelic gene expression landscapes and expression bias pattern shape the transcriptome of the clonal Amazon molly
- Yuan Lu,
- David Bierbach,
- Jenny Ormanns,
- Wesley C. Warren,
- Ronald B. Walter,
- and Manfred Schartl
Genome Res. March 2021 31: 372-379; Published in Advance February 5, 2021, doi:10.1101/gr.268870.120
...is allelic expression bias. An earlier study (Warren et al. 2018) revealed that in P. formosa 5% of the genes show allele-specific expression from one of the ancestral parental s. Therefore, in this study, we aim to compare allelic expression divergence intra-cohort or inter-cohort of clonal Amazon molly...
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Research: Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F₁ hybrids
- Carina F. Mugal,
- Mi Wang,
- Niclas Backström,
- David Wheatcroft,
- Murielle Ålund,
- Marie Sémon,
- S. Eryn McFarlane,
- Ludovic Dutoit,
- Anna Qvarnström,
- and Hans Ellegren
Genome Res. December 2020 30: 1727-1739; Published in Advance November 3, 2020, doi:10.1101/gr.254508.119
...for crosses of species/inbred lines with substantially divergent s, to study regulatory evolution. Instead, we used a protocol suitable for natural populations, where polymorphism is abundant, that tests for an association between differential gene expression and allele-specific expression in F1 hybrids...
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Research: Drought responsive gene expression regulatory divergence between upland and lowland ecotypes of a perennial C₄ grass
- John T. Lovell,
- Scott Schwartz,
- David B. Lowry,
- Eugene V. Shakirov,
- Jason E. Bonnette,
- Xiaoyu Weng,
- Mei Wang,
- Jenifer Johnson,
- Avinash Sreedasyam,
- Christopher Plott,
- Jerry Jenkins,
- Jeremy Schmutz,
- and Thomas E. Juenger
Genome Res. April 2016 26: 510-518; Published in Advance March 7, 2016, doi:10.1101/gr.198135.115
.... 2008; Chen 2010). Inference of cis- and cis-treatment gene expression G×E via a linear model We quantified allele-specific expression for 16,465 genes by the presence of HAL2- or FIL2-specific single nucleotide polymorphisms.We then partitioned the variance of ASE into that attributable to allelic...
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Research: Neonatal DNA methylation profile in human twins is specified by a complex interplay between intrauterine environmental and genetic factors, subject to tissue-specific influence
- Lavinia Gordon,
- Jihoon E. Joo,
- Joseph E. Powell,
- Miina Ollikainen,
- Boris Novakovic,
- Xin Li,
- Roberta Andronikos,
- Mark N. Cruickshank,
- Karen N. Conneely,
- Alicia K. Smith,
- Reid S. Alisch,
- Ruth Morley,
- Peter M. Visscher,
- Jeffrey M. Craig,
- and Richard Saffery
Genome Res. August 2012 22: 1395-1406; Published in Advance July 16, 2012, doi:10.1101/gr.136598.111
...revealed a general association between methylation of genes involved in metabolism and biosynthesis, providing further support for epigenetic change in the previously described link between low birth weight and increasing risk for cardiovascular, metabolic, and other complex diseases. Finally, comparison...
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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
...-specific expression of the distal Brd2 gene (Table 2; Yang et al. 2022). Strikingly, transient allele-specific expression can also have long-term effects, as illustrated by the Zdbf2 locus, whose regulatory mechanism is conserved between humans and mice. A transient gDMR modifies the epigenetic landscape upstream...

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