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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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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
...aging dimensionWe developed a positive epigenetic drift score (EDS_POS) using 204 independent CpGs, each more than 500 kbp apart (Supplemental Table S4). These CpGs were selected from the 49,877 positive drift-CpGs identified in NSPT, based on their smallest Fisher combined P-values across NSPT, CAS...
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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
...: arturo.mari-ordonez@gmi.oeaw.ac.atAbstractA handful of model plants have provided insight into silencing of transposable elements (TEs) through RNA-directed DNA methylation (RdDM). Guided by 24 nt long small-interfering RNAs (siRNAs), this epigenetic regulation installs DNA methylation and histone...
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Research: Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries
- Shaoqiang Hu,
- Xiangguo Zeng,
- Yuguo Liu,
- Yongping Li,
- Minghao Qu,
- Wen-Biao Jiao,
- Yongchao Han,
- and Chunying Kang
Genome Res. October 2024 34: 1582-1594; Published in Advance October 15, 2024, doi:10.1101/gr.279378.124
....71%–8.03%) in regenerated plants, and hypoCG-DMRs are more heritable after sexual reproduction. A high-quality haplotype-resolved is assembled for the strawberry cultivar “Beni hoppe.” The 12 “Beni hoppe” individuals randomly selected from different locations show 4731–6005 mutations relative to the reference...
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Research: The rate and spectrum of new mutations in mice inferred by long-read sequencing
- Eugenio López-Cortegano,
- Jobran Chebib,
- Anika Jonas,
- Anastasia Vock,
- Sven Künzel,
- Peter D. Keightley,
- and Diethard Tautz
Genome Res. January 2025 35: 43-54; Published in Advance December 2, 2024, doi:10.1101/gr.279982.124
...for evolutionary studies (Guénet and Bonhomme 2003; Harr et al. 2016). To gain a deeper understanding of mammal evolution, we conducted an MA experiment in mice. Lines were maintained by full-sib mating to minimize the effective population size and the effectiveness of selection acting on newly arising mutations...
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Research: Transcriptional modulation unique to vulnerable motor neurons predicts ALS across species and SOD1 mutations
- Irene Mei,
- Susanne Nichterwitz,
- Melanie Leboeuf,
- Jik Nijssen,
- Isadora Lenoel,
- Dirk Repsilber,
- Christian S. Lobsiger,
- and Eva Hedlund
Genome Res. September 2025 35: 1975-1991; Published in Advance July 17, 2025, doi:10.1101/gr.279501.124
...stem cell–derived SOD1E100G MNs and shows that dysregulation of VGF, INA, and PENK is a strong disease predictor across species and SOD1 mutations. Our study reveals MN population-specific gene expression and temporal disease-induced regulation that together provide a basis to explain ALS selective...
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Research: Chromatin structure influences rate and spectrum of spontaneous mutations in Neurospora crassa
- Mariana Villalba de la Peña,
- Pauliina A.M. Summanen,
- Martta Liukkonen,
- and Ilkka Kronholm
Genome Res. April 2023 33: 599-611; Published in Advance March 15, 2023, doi:10.1101/gr.276992.122
...with other evolutionary mechanisms, is understood mostly from population genetic data, rather than from direct observations of mutation, with a few exceptions (e.g., Monroe et al. 2022). There are some tests for selection, such as dN/dS ratios, which are not affected by the mutation rate. However, tests...
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Research: Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations
- Alicja Pacholewska,
- Matthias Lienhard,
- Mirko Brüggemann,
- Heike Hänel,
- Lorina Bilalli,
- Anja Königs,
- Felix Heß,
- Kerstin Becker,
- Karl Köhrer,
- Jesko Kaiser,
- Holger Gohlke,
- Norbert Gattermann,
- Michael Hallek,
- Carmen D. Herling,
- Julian König,
- Christina Grimm,
- Ralf Herwig,
- Kathi Zarnack,
- and Michal R. Schweiger
Genome Res. November 2024 34: 1832-1848; Published in Advance September 13, 2024, doi:10.1101/gr.279327.124
...,2,14, Ralf Herwig3,14, Kathi Zarnack4,14 and Michal R. Schweiger1,2,14 1Institute for Translational Epigenetics, Faculty of Medicine, University of Cologne, 50931 Cologne, Germany; 2Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine, University of Cologne, 50931 Cologne, Germany; 3Department...
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Research: Modeling alternative translation initiation sites in plants reveals evolutionarily conserved cis-regulatory codes in eukaryotes
- Ting-Ying Wu,
- Ya-Ru Li,
- Kai-Jyun Chang,
- Jhen-Cheng Fang,
- Daisuke Urano,
- and Ming-Jung Liu
Genome Res. February 2024 34: 272-285; Published in Advance March 13, 2024, doi:10.1101/gr.278100.123
...the selection of the translation initiation site (TIS) in the mRNA. The choice of TIS determines the coding sequence (CDS) of mRNA and ensures the accurate and timely production of a desired protein. This mechanism enables plants to rapidly respond to developmental cues and environmental stress (Merchante et al...
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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
...[ITH]) in gene expression and their functional phenotypes that cannot always be explained by mutations or structural variations in their DNA. Nongenetic basis for ITH suggests a potential role for epigenetic mechanisms driving transcriptomic/phenotypic heterogeneity (Brock et al. 2009). Epigenetic...
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