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Research: ACTB methylation regulates SMARCA4 genomic occupancy to promote translation and reduce adhesion in colorectal cancer cells
- Elina Abaev-Schneiderman,
- Linh Nguyen,
- Raz Shalev,
- Tzofit Elbaz Biton,
- Anand Chopra,
- Giritharan Jagadeesan,
- Daniel Sevilla-Sanchez,
- Nili Tickotsky Moskovitz,
- Liron Levin,
- Michal Feldman,
- Capucine Van Rechem,
- and Dan Levy
Genome Res. April 2026 36: 684-694; Published in Advance March 25, 2026, doi:10.1101/gr.280534.125
....ResultsMethylated ACTB regulates gene transcriptionIt was previously shown that depletion of SETD3 completely eliminates ACTB methylation on H73 (Wilkinson et al. 2019). To examine if ACTB H73 methylation regulates its genomic distribution, we performed Cleavage Under Targets and Release Using Nuclease (CUT&RUN) assays...
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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
...samples. See also Supplemental Figures S3–S7.The genomic composition surrounding MYH6 and MYH7 is preserved between humans and mice (Fig. 2A; Supplemental Fig. S5A). We identified three noncoding regions (R1–R3, M3, and C3) that interact with MYH6 and likely influence MYH6 expression (Fig. 2A...
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Research: Transcription and potential functions of a novel XIST isoform in male peripheral glia
- Kevin S. O'Leary,
- Meng-Yen Li,
- Kevyn Jackson,
- Lijie Shi,
- Elena Ezhkova,
- Bernice E. Morrow,
- and Deyou Zheng
Genome Res. February 2026 36: 257-274; Published in Advance December 12, 2025, doi:10.1101/gr.280832.125
...). Through interactions between its functional domains (repeat regions A–E) and various proteins, such as Polycomb Repressive Complexes (PRC1/2), CIZ1, and YY1, the XIST ribonucleoprotein complex silences one copy of the X Chromosome in female somatic tissues (Loda and Heard 2019; Jacobson et al. 2022...
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Resource: PWAS Hub for exploring gene-based associations of common complex diseases
- Guy Kelman,
- Roei Zucker,
- Nadav Brandes,
- and Michal Linial
Genome Res. October 2024 34: 1674-1686; Published in Advance October 15, 2024, doi:10.1101/gr.278916.123
...in recent years due to the increased scale of resources with rich genomic and clinical data (Bernabeu et al. 2021).The PWAS Hub leverages the results of PWAS for most of the abundant complex diseases and conditions represented in UKB (e.g., asthma, hypertension, type 2 diabetes). It encompasses the human...
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Resource: Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding
- Kai Li,
- Melissa L. Smith,
- J. Chris Blazier,
- Kelli J. Kochan,
- Jonathan M.D. Wood,
- Kerstin Howe,
- Anne E. Kwitek,
- Melinda R. Dwinell,
- Hao Chen,
- Julia L. Ciosek,
- Patrick Masterson,
- Terence D. Murphy,
- Theodore S. Kalbfleisch,
- and Peter A. Doris
Genome Res. November 2024 34: 2081-2093; Published in Advance November 8, 2024, doi:10.1101/gr.279292.124
...on Chr 19 shows aligned transcript data across its extent. This is in contrast to newly incorporated centromeric regions in which no aligned transcripts were observed. To investigate further, we examined whether the included region might be composed of expanded genomic sequences with high similarity...
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Method: Exon Nomenclature And Classification of Transcripts (ENACT) provides a systematic framework to annotate exon attributes
- Paras Verma,
- Deeksha Thakur,
- Deepanshi Awasthi,
- and Shashi Bhushan Pandit
Genome Res. June 2025 35: 1440-1455; Published in Advance May 7, 2025, doi:10.1101/gr.279878.124
...initiates from this exon (in this case, exon 3), value would be incremented by one. The EUID of the end exon up to which the intron genomic region has been retained (in this case, exon 4). An AIF1 gene instance illustrating such cases is shown in Supplemental Figure S2.Through the above...
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Method: Matrix sketching framework for linear mixed models in association studies
- Myson Burch,
- Aritra Bose,
- Gregory Dexter,
- Laxmi Parida,
- and Petros Drineas
Genome Res. September 2024 34: 1304-1311; Published in Advance September 4, 2024, doi:10.1101/gr.279230.124
...Myson Burch1,3, Aritra Bose1,3, Gregory Dexter2, Laxmi Parida1 and Petros Drineas2 1Computational Genomics, IBM T.J. Watson Research Center, Yorktown Heights, New York 10598, USA; 2Computer Science Department, Purdue University, West Lafayette, Indiana 47907, USA ↵3 These authors contributed...
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Resource: GenomeMUSter mouse genetic variation service enables multitrait, multipopulation data integration and analysis
- Robyn L. Ball,
- Molly A. Bogue,
- Hongping Liang,
- Anuj Srivastava,
- David G. Ashbrook,
- Anna Lamoureux,
- Matthew W. Gerring,
- Alexander S. Hatoum,
- Matthew J. Kim,
- Hao He,
- Jake Emerson,
- Alexander K. Berger,
- David O. Walton,
- Keith Sheppard,
- Baha El Kassaby,
- Francisco Castellanos,
- Govindarajan Kunde-Ramamoorthy,
- Lu Lu,
- John Bluis,
- Sejal Desai,
- Beth A. Sundberg,
- Gary Peltz,
- Zhuoqing Fang,
- Gary A. Churchill,
- Robert W. Williams,
- Arpana Agrawal,
- Carol J. Bult,
- Vivek M. Philip,
- and Elissa J. Chesler
Genome Res. January 2024 34: 145-159; Published in Advance January 30, 2024, doi:10.1101/gr.278157.123
...region with a data-driven approach that incorporates local phylogenetic information and the Viterbi algorithm, as implemented in HaploQA (https://haploqa.jax.org). For each target strain in each region, a strain-specific “held-out” test set was randomly selected and not used in the imputation process...
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Research: Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis
- Olga M. Sigalova,
- Mattia Forneris,
- Frosina Stojanovska,
- Bingqing Zhao,
- Rebecca R. Viales,
- Adam Rabinowitz,
- Fayrouz Hammal,
- Benoît Ballester,
- Judith B. Zaugg,
- and Eileen E.M. Furlong
Genome Res. May 2025 35: 1138-1153; Published in Advance April 15, 2025, doi:10.1101/gr.279652.124
..., TF binding for each factor is highly variable across genotypes, as shown for two loci for Twist and Mef2 occupancy (Fig. 1F).Effects of genetic variation on TF binding are extensive and preferably detected in genomic regions with less bufferingTo disentangle the impact of genetic variation on TF...
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PERSPECTIVE: Impact of genomics on research in the rat
- Jozef Lazar,
- Carol Moreno,
- Howard J. Jacob,
- and Anne E. Kwitek
Genome Res. December 2005 15: 1717-1728; doi:10.1101/gr.3744005
..., in order to substitute a selected genomic region from the BN rat. ( B ) A male and female rat, selected by genotyping for this specific target region containing the phenotype of interest, are then mated. Twenty-five percent of the offspring from this cross will be homozygous for this region. These rats...

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