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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
...similar to that of canonically active epigenetic features, the proportions of promoters marked by the other modifications are minimal (Supplemental Fig. S3). When analyzed on a per-tissue basis, the profiles of active histone modifications and chromatin accessibility exhibit a consistent pattern across...
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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
...incompletely understood despite their relevance to facioscapulohumeral muscular dystrophy (FSHD). Current FSHD molecular testing relies on complex, multistep and low-resolution assays, which aim to identify contractions on permissive haplotypes (FSHD type 1) or epigenetic reactivation due to pathogenic...
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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
..., College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh 11452, Kingdom Saudi Arabia ↵10 These authors contributed equally to this work. Corresponding authors: fliu@nauss.edu.sa, wangsijia@picb.ac.cn, dr_xiamingfeng@163.comAbstractEpigenetic drift refers to the gradual...
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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
...&Tag to map a variety of histone PTMs, including the euchromatin marks H3K9ac, H3K14ac, and H3K27ac, facultative heterochromatin mark H3K27me3, and constitutive heterochromatin marks H3K9me2 and H3K9me3. We also used ChIP-seq to profile the H3K9 methylation binding protein CBX1.Scaling all LADs to a uniform...
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Research: CTCF looping is established during gastrulation in medaka embryos
- Ryohei Nakamura,
- Yuichi Motai,
- Masahiko Kumagai,
- Candice L. Wike,
- Haruyo Nishiyama,
- Yoichiro Nakatani,
- Neva C. Durand,
- Kaori Kondo,
- Takashi Kondo,
- Tatsuya Tsukahara,
- Atsuko Shimada,
- Bradley R. Cairns,
- Erez Lieberman Aiden,
- Shinichi Morishita,
- and Hiroyuki Takeda
Genome Res. June 2021 31: 968-980; Published in Advance May 18, 2021, doi:10.1101/gr.269951.120
...). Compartment domains are formed by cosegregation of chromatin intervals with similar histone marks, which is a phenomenon more generally known as compartmentalization (Lieberman-Aiden et al. 2009; Rao et al. 2014). Genome architecture plays a critical role in gene regulation, but how architecture...
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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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Method: TFcomb identifies transcription factor combinations for cellular reprogramming based on single-cell multiomics data
- Chen Li,
- Sijie Chen,
- Yixin Chen,
- Haiyang Bian,
- Minsheng Hao,
- Lei Wei,
- and Xuegong Zhang
Genome Res. June 2025 35: 1429-1439; Published in Advance April 10, 2025, doi:10.1101/gr.279955.124
...(Cebpa, Cebpb, and Spi1) and s5 (POU5F1 and SOX2) are marked in red. (D) Comparison between the single-TF list and double-TF list of TFcomb in case s5. The single ground-truth reprogramming TFs in the rows and the double ground-truth reprogramming TFs in the columns are both marked in red. (E) Ranked TF...
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Research: Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza
- Rodolphe Dombey,
- Daniel Buendía-Ávila,
- Verónica Barragán-Borrero,
- Laura Diezma-Navas,
- Arturo Ponce-Mañe,
- José Mario Vargas-Guerrero,
- Rana Elias,
- and Arturo Marí-Ordóñez
Genome Res. March 2025 35: 522-544; Published in Advance March 4, 2025, doi:10.1101/gr.279532.124
...and Madhani 2018). Heterochromatin is generally characterized by repressive epigenetic marks, prominently DNA methylation (5′methylcytosine [5mC]), histone modifications such as histone H3 lysine-9 mono- and dimethylation (H3K9me1/H3K9me2, constitutive heterochromatin) or histone H3 lysine-27 triple...
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Research: Broad domains of histone marks in the highly compact Paramecium macronuclear genome
- Franziska Drews,
- Abdulrahman Salhab,
- Sivarajan Karunanithi,
- Miriam Cheaib,
- Martin Jung,
- Marcel H. Schulz,
- and Martin Simon
Genome Res. April 2022 32: 710-725; Published in Advance March 9, 2022, doi:10.1101/gr.276126.121
..., although a deeper biochemical insight in the MAC chromatin organization is still missing. The same holds true for the presence of classical repressive histone marks in the vegetative MAC, raising the question of how gene repression is regulated. Another epigenetic mark, 5-methylcytosine, is known...
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Method: Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression
- Howard J. Womersley,
- Daniel Muliaditan,
- Ramanuj DasGupta,
- and Lih Feng Cheow
Genome Res. January 2025 35: 162-177; Published in Advance December 2, 2024, doi:10.1101/gr.279105.124
...amplification.Genetic–epigenetic alterations correlate with changes in gene expressionBecause our data suggested that genetic drivers such as YAP1 amplification could lead to changes in the epi, we further explored how changes in gene copy number (CN) and the combination of active histone marks, such as H3K4me3...
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