Searching journal content for articles similar to Barutcu et al. 26 (9): 1188.

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  1. 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
    ...stimulates the ATPase activity of the SMARCA4 subunit and is required for BAF complex association with the nuclear matrix (Falahzadeh et al. 2015; Sen et al. 2024). The BAF complex plays a crucial role in development and differentiation by directly regulating the chromatin state of critical genes to oppose...
  2. Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
    • Paul Ashford,
    • Alexander M. Frankell,
    • Zofia Piszka,
    • Camilla S.M. Pang,
    • Mahnaz Abbasian,
    • Maise Al Bakir,
    • Mariam Jamal-Hanjani,
    • Nicholas McGranahan,
    • Charles Swanton,
    • and Christine A. Orengo
    Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
    ...genes, with an average of more than 10 FIEs per gene. Only seven genes had FIEs identified in more than five tumors, all of which were known cancer genes: TP53 (n = 74 FIEs), PIK3CA (28), CDKN2A (13), KRAS (90), SMARCA4 (7), LUAD-specific EGFR (10), and BRAF (8). Using driver mutations classified...
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  3. Method: Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie
    • Krzysztof H. Banecki,
    • Haoxi Chai,
    • Yijun Ruan,
    • and Dariusz Plewczynski
    Genome Res. April 8, 2026 ; Published in Advance April 8, 2026, doi:10.1101/gr.280985.125
    ...) is a high-throughput method that simultaneously measures gene expression, chromatin accessibility, and chromatin interactions in single cells. By leveraging a microfluidic platform, it can analyze 6000−8000 cells in a single reaction, providing insights into the 3D epigenomic mechanisms that regulate...
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  4. Research: Loss of epigenetic suppression of retrotransposons with oncogenic potential in aging mammary luminal epithelial cells
    • Parijat Senapati,
    • Masaru Miyano,
    • Rosalyn W. Sayaman,
    • Mudaser Basam,
    • Amy Leung,
    • Mark A. LaBarge,
    • and Dustin E. Schones
    Genome Res. August 2023 33: 1229-1241; Published in Advance July 18, 2023, doi:10.1101/gr.277511.122
    ...on TE silencing and the functional consequences of this have remained unclear. To assess the epigenetic regulation of TEs in aging, we profiled DNA methylation in human mammary luminal epithelial cells (LEps)—a key cell lineage implicated in age-related breast cancers—from younger and older women. We...
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  5. Method: Recovering gene regulatory networks in single-cell multi-omics data with PRISM-GRN
    • Wenhao Zhang,
    • Lan Cao,
    • Xiaoxuan Gu,
    • Yongyu Long,
    • and Ying Wang
    Genome Res. January 2026 36: 142-158; Published in Advance October 9, 2025, doi:10.1101/gr.280757.125
    ...2005; Chen and Rajewsky 2007). The intricate mechanisms underlying gene regulation form the basis for cellular function and behavior (Karlebach and Shamir 2008). Epigenetic modifications influence chromatin structure and accessibility, mutually affecting TF binding and the assembly of GRNs, which...
  6. Method: Statistically rigorous and computationally efficient chromatin stripe detection with Quagga
    • Fan Feng,
    • Sean Moran,
    • Anders S. Hansen,
    • Xiaotian Zhang,
    • and Jie Liu
    Genome Res. January 2026 36: 159-168; Published in Advance November 12, 2025, doi:10.1101/gr.280132.124
    ...features in which a singular loop anchor interacts with a contiguous region of DNA so, at the bulk sequencing level, it appears as a long stripe on chromatin contact matrices. Stripes are thought to play an important role in gene regulation and have been implicated in regulating a cell's lineage...
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  7. Method: Robust and efficient annotation of cell states through gene signature scoring
    • Laure Ciernik,
    • Agnieszka Kraft,
    • Florian Barkmann,
    • Josephine Yates,
    • and Valentina Boeva
    Genome Res. March 2026 36: 630-644; Published in Advance February 18, 2026, doi:10.1101/gr.280926.125
    ...epithelial-to-mesenchymal transition. Overall, ANS provides a robust and reliable gene signature scoring framework, significantly improving the accuracy of score-based annotation of cell types and states in single-cell studies.High-throughput single-cell RNA sequencing (scRNA-seq) is a powerful technology...
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  8. Method: Analysis of coding gene expression from small RNA sequencing
    • Aygun Azadova,
    • Anthonia Ekperuoh,
    • Greg N. Brooke,
    • and Antonio Marco
    Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
    ...- and downregulated in tumors (Fig. 3; Supplemental Fig. 4). The functional annotation of upregulated genes from this analysis reveals an enrichment in functional categories (within the biological process domain in Gene Ontology) related with cell proliferation, as expected for cancer samples (Table 3). Also...
  9. 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
    ...regulation can be inferred from experimentally measured changes in chromatin accessibility at carefully selected gene loci. For this purpose, Förster resonance energy transfer combined with fluorescence in situ hybridization (FRET-FISH) was recently developed (Mota et al. 2022). This method takes advantage...
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  10. Research: Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits
    • Kevin W. Currin,
    • Hannah J. Perrin,
    • Gautam K. Pandey,
    • Abdalla A. Alkhawaja,
    • Swarooparani Vadlamudi,
    • Annie E. Musser,
    • Amy S. Etheridge,
    • K. Alaine Broadaway,
    • Jonathan D. Rosen,
    • Arushi Varshney,
    • Amarjit S. Chaudhry,
    • Paul J. Gallins,
    • Fred A. Wright,
    • Yi-hui Zhou,
    • Stephen C.J. Parker,
    • Laura M. Raffield,
    • Erin G. Schuetz,
    • Federico Innocenti,
    • and Karen L. Mohlke
    Genome Res. July 2025 35: 1485-1502; Published in Advance May 20, 2025, doi:10.1101/gr.279741.124
    ...Peaks with a GWAS colocalization, 487 had a predicted target gene, 462 contained a disrupted motif, and 226 had both target genes and disrupted motifs (Supplemental Table 23). We identified 231 caQTL signals that colocalized with both GWAS and eQTL signals, consistent with joint genetic regulation of chromatin...
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