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Research: Epigenetic characterization of pseudogenes across human tissues
- Yunzhe Jiang,
- Beatrice Borsari,
- and Mark Gerstein
Genome Res. April 15, 2026 gr.280768.125; Published in Advance April 15, 2026, doi:10.1101/gr.280768.125
...a modest enrichment of H3K4me3 peaks in the 1,000 bp promoter region downstream of the TSS (McNemar test, pvalue = 0.03, FDR-adjusted). Next, we identified transcription factor motifs that could potentially mediate processed pseudogene transcription. We found that 20% of processed pseudogene promoters...
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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
...is characterized by permissive marks, including H3K4me2/me3 (Fournier et al. 2002; McEwen and Ferguson-Smith 2010). Accordingly, at the -wide level, ICRs are discrete regions with a four-mark signature comprising partial DNA methylation, H3K4me3, H3K9me3, and H4K20me3 in somatic cells.With the exception...
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Method: Complete genetic and epigenetic architecture of D4Z4 macrosatellites in FSHD, BAMS, and reference cohorts with D4Z4End2End
- Lucinda C. Xiao,
- Ayush Semwal,
- Brianna St John,
- Kathleen Zeglinski,
- Shian Su,
- James Lancaster,
- Shifeng Xue,
- Bruno Reversade,
- Matthew E. Ritchie,
- Frédérique Magdinier,
- Marnie E. Blewitt,
- and Quentin Gouil
Genome Res. April 2026 36: 827-848; Published in Advance March 23, 2026, doi:10.1101/gr.280907.125
...of each allele, and in exploring cell-to-cell epigenetic variability or indeed genetic mosaicism.To address this, we used Cas9-targeted sequencing to enrich for the 4q and 10q D4Z4 regions, aiming to capture the whole set of alleles in each patient. We designed guide RNAs targeting regions upstream...
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Research: Dynamics of broad H3K4me3 domains uncover an epigenetic switch between cell identity and cancer-related genes
- Mohamed Belhocine,
- Mathieu Simonin,
- José David Abad Flores,
- Agata Cieslak,
- Iris Manosalva,
- Lydie Pradel,
- Charlotte Smith,
- Eve-Lyne Mathieu,
- Guillaume Charbonnier,
- Joost H.A. Martens,
- Hendrik G. Stunnenberg,
- Muhammad Ahmad Maqbool,
- Aneta Mikulasova,
- Lisa J. Russell,
- Daniel Rico,
- Denis Puthier,
- Pierre Ferrier,
- Vahid Asnafi,
- and Salvatore Spicuglia
Genome Res. July 2022 32: 1328-1342; Published in Advance June 23, 2021, doi:10.1101/gr.266924.120
...be contained in the spread of epigenetic modifications over a genomic locus. Large megabase-sized chromatin domains have been described for the repressive chromatin mark H3K9me3 in senescence cells spanning large chromosomal regions (Soufi et al. 2012) or activating H3K4me3 in mammalian oocytes (Dahl 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
...with newly generated ATAC-seq data from iPSC-derived NPCs (Wells et al. 2023). Active STARR-seq regions showed higher ATAC-seq signals than either randomly selected regions or low-scoring STARR-seq regions (Supplemental Fig. S3; Supplemental Table S5; Supplemental Methods), providing additional support...
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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
...promoter-like and active, with a reduction in H3K36me3 and an accumulation of H3K4me3 and H3K27ac (Fig. 7D). This result is consistent with the previously proposed aging model, where reduced H3K36me3 levels within gene bodies inhibit the recruitment of KDM5B and DNMT3B to these regions, resulting...
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Research: Characterization of the distribution and dynamics of chromatin states in the C. elegans germline reveals substantial H3K4me3 remodeling during oogenesis
- Mariateresa Mazzetto,
- Lauren E. Gonzalez,
- Nancy Sanchez,
- and Valerie Reinke
Genome Res. January 2024 34: 57-69; Published in Advance December 26, 2023, doi:10.1101/gr.278247.123
...(state 3) in IGN, whereas regions in the “H3K4me3-only” state E gain H3K36me3 and become the active states 9 (TSS–gene body) and 10 (active transcription) in IGN. At the resolution of individual genes, we also found many changes between germline and somatic epigenetic profiles (Supplemental Fig. S2D...
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Research: Estrogen-induced chromatin looping changes identify a subset of functional regulatory elements
- Hosiana Abewe,
- Alexandra Richey,
- Jeffery M. Vahrenkamp,
- Matthew Ginley-Hidinger,
- Craig M. Rush,
- Noel Kitchen,
- Xiaoyang Zhang,
- and Jason Gertz
Genome Res. March 2025 35: 393-403; Published in Advance March 3, 2025, doi:10.1101/gr.279699.124
...) interactions, and these interactions are commonly altered in cancer. Yet, the functional relationship between changes in 3D interactions associated with regulatory regions and differential gene expression appears context-dependent. In this study, we used HiChIP to capture changes in 3D interactions between...
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Research: Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancers
- Aneta Mikulasova,
- Daniel Kent,
- Marco Trevisan-Herraz,
- Nefeli Karataraki,
- Kent T.M. Fung,
- Cody Ashby,
- Agata Cieslak,
- Shmuel Yaccoby,
- Frits van Rhee,
- Maurizio Zangari,
- Sharmilan Thanendrarajan,
- Carolina Schinke,
- Gareth J. Morgan,
- Vahid Asnafi,
- Salvatore Spicuglia,
- Chris A. Brackley,
- Anne E. Corcoran,
- Sophie Hambleton,
- Brian A. Walker,
- Daniel Rico,
- and Lisa J. Russell
Genome Res. July 2022 32: 1343-1354; Published in Advance December 21, 2021, doi:10.1101/gr.276042.121
...) having no detectable translocation involving any of the Ig loci (Supplemental Table S5). No cell lines or patients had an IGH-CCND1 rearrangement detected by targeted or sequencing; therefore, as expected, we did not observe an aberrant H3K4me3-BD or an increase in mRNA transcript levels for CCND1...
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Research: Epigenetic and evolutionary features of ape subterminal heterochromatin
- DongAhn Yoo,
- Katherine M. Munson,
- and Evan E. Eichler
Genome Res. January 2026 36: 38-49; Published in Advance October 22, 2025, doi:10.1101/gr.280987.125
...insertions and lineage-specific duplicated genes. Our findings suggest independent evolution of subterminal caps converging on a common genetic and epigenetic structure that promoted ectopic exchange as well as the emergence of novel genes at transition regions between euchromatin and heterochromatin...
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