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Research: Variation in histone configurations correlates with gene expression across nine inbred strains of mice
- Anna L Tyler,
- Catrina Spruce,
- Romy Kursawe,
- Annat Haber,
- Robyn L Ball,
- Wendy A Pitman,
- Alexander D Fine,
- Narayanan Raghupathy,
- Michael Walker,
- Vivek M Philip,
- Christopher L Baker,
- J. Matthew Mahoney,
- Gary A. Churchill,
- Jennifer J Trowbridge,
- Michael L Stitzel,
- Kenneth Paigen,
- Petko M Petkov,
- and Gregory W Carter
Genome Res. May 22, 2023 gr.277467.122; Published in Advance May 22, 2023, doi:10.1101/gr.277467.122
...and was associated with variation in gene expression across strains. We found that epigenetic24 state imputed into a population of DO mice recapitulated the association with gene expression25 seen in the founders suggesting that both histone modifications and DNA methylation are highly26 heritable mechanisms of gene...
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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
..., a particular gene of interest (GOI) remains a persistent experimental and conceptual challenge. This gene-centric question is complicated by the multilayered regulatory environment in which each gene resides, comprising 3D chromatin structure, enhancer–promoter looping, DNA accessibility, histone modifications...
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Research: A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress
- Taylor Anglen,
- Irene M. Kaplow,
- Baekgyu Choi,
- Enya Dewars,
- Robin M. Perelli,
- Kevin T. Hagy,
- Duc Tran,
- Megan E. Ramaker,
- Svati H. Shah,
- Inkyung Jung,
- Andrew P. Landstrom,
- Ravi Karra,
- Yarui Diao,
- and Charles A. Gersbach
Genome Res. November 2025 35: 2418-2432; Published in Advance October 22, 2025, doi:10.1101/gr.280825.125
..., and cells maintain higher levels of MYH6.Lastly, we identified cardiomyopathy-associated genetic variants within R3 (Supplemental Fig. S11A). This underscores the impact of genetic variation on complex human traits. Allelic imbalance of disease-related genes has been observed in patients with hypertrophic...
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Resource: Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise
- Aliza B. Rubenstein,
- Gregory R. Smith,
- Zidong Zhang,
- Xi Chen,
- Toby L. Chambers,
- Frederique Ruf-Zamojski,
- Natalia Mendelev,
- Wan Sze Cheng,
- Michel Zamojski,
- Mary Anne S. Amper,
- Venugopalan D. Nair,
- Andrew R. Marderstein,
- Stephen B. Montgomery,
- Olga G. Troyanskaya,
- Elena Zaslavsky,
- Todd Trappe,
- Scott Trappe,
- and Stuart C. Sealfon
Genome Res. July 2025 35: 1664-1677; Published in Advance May 20, 2025, doi:10.1101/gr.280051.124
...overlapping and fiber-type-specific regulated genes and chromatin regions (Fig. 2C–F). Intermediate fibers also had a high number of DEGs but had a comparatively lower number of DARs. Although the reason for this apparent discrepancy is uncertain, it could be related to the heterogeneous nature...
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Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
- Carolina Monzó,
- Adam Frankish,
- and Ana Conesa
Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
...genomic variation and its effect on phenotypes and gene regulation. Nature 477: 289–294. doi:10.1038/nature10413 ↵Keil N, Monzó C, McIntyre L, Conesa A. 2025. Quality assessment of long read data in multisample lrRNA-seq experiments with SQANTI-reads. Genome Res (this issue) 35: 987–998. doi:10.1101/gr...
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Research: De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes
- Basanta Bista,
- Laura González-Rodelas,
- Lucía Álvarez-González,
- Zhi-qiang Wu,
- Eugenia E. Montiel,
- Ling Sze Lee,
- Daleen B. Badenhorst,
- Srihari Radhakrishnan,
- Robert Literman,
- Beatriz Navarro-Dominguez,
- John B. Iverson,
- Simon Orozco-Arias,
- Josefa González,
- Aurora Ruiz-Herrera,
- and Nicole Valenzuela
Genome Res. October 2024 34: 1553-1569; Published in Advance October 16, 2024, doi:10.1101/gr.279443.124
...as reference for comparison. (C) Circos plots (of sequences >3 kbp) depicting genomic chromosomal syntenies and comparative genomic characteristics (Log10 of normalized Transcripts Per Million—TPM—gene expression, GC, and gene content) between ASP and STR. (D) GC content, gene density, and average gene length...
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Research: Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles
- Xuejing Wang and
- Gerald Heckel
Genome Res. June 2024 34: 851-862; Published in Advance July 2, 2024, doi:10.1101/gr.278487.123
...), as described at http://creativecommons.org/licenses/by-nc/4.0/.References ↵The 1000 Genomes Project Consortium. 2015. A global reference for human genetic variation. Nature 526: 68–74. doi:10.1038/nature15393 ↵Adler GH, Levins R. 1994. The island syndrome in rodent populations. Q Rev Biol 69: 473–490. doi:10...
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Research: Transposons contribute to the functional diversification of the head, gut, and ovary transcriptomes across Drosophila natural strains
- Marta Coronado-Zamora and
- Josefa González
Genome Res. September 2023 33: 1541-1553; Published in Advance October 4, 2023, doi:10.1101/gr.277565.122
...of TEs in the studied (Lipatov et al. 2005; Treiber and Waddell 2020), in this work, we took advantage of the availability of high-quality assemblies, annotations, transcriptomes, and histone mark enrichments for five natural strains to carry out an in-depth analysis of gene–TE chimeric transcripts (Rech...
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Research: Distinct contributions of DNA methylation and histone acetylation to the genomic occupancy of transcription factors
- Martin Cusack,
- Hamish W. King,
- Paolo Spingardi,
- Benedikt M. Kessler,
- Robert J. Klose,
- and Skirmantas Kriaucionis
Genome Res. October 2020 30: 1393-1406; Published in Advance September 22, 2020, doi:10.1101/gr.257576.119
...Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ, United Kingdom Corresponding author: skirmantas.kriaucionis@ludwig.ox.ac.ukAbstractEpigenetic modifications on chromatin play important roles in regulating gene expression. Although chromatin states are often governed by multilayered...
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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
...-by-environment interactions can also alter gene expression patterns in a dynamic and tissue-specific manner without modifying the underlying nucleotide sequence; these effects are missed in a typical sequence-based method. Thus, an allele-specific approach is required to directly measure how cis-regulatory variation impacts...
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