Searching journal content for articles similar to Cusack et al. 30 (10): 1393.

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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
...is also present in the nucleus where it participates in the regulation of RNA processing and export. Its roles also extend to the regulation of transcription and DNA repair (Hurst et al. 2019). ACTB associates with both RNA polymerase II (Pol II) (Pestic-Dragovich et al. 2000) and RNA polymerase III (Pol...
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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
...). Data was filtered to remove reads mapping to mitochondrial DNA or unlocalized or unplaced contigs. Individual replicates were merged and converted to bedGraph or bigWig format for viewing on the Integrative Genomics Viewer (IGV) (Robinson et al. 2011) and for downstream analysis.For LAD calling, lamin...
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Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
...me2 but high DNA methylation (except state 20, which is enriched in transcriptional start sites), corresponding to >80% of SUVH1 and SUVH3-binding sites; states 14 and 15 (5034 loci; 7.8% of the ), long TEs enriched in DNA methylation and H3K9me2, contributing to 25% of MBD5 and MBD6 targets, which...
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Method: Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
- Haiyue Liu and
- Lea H. Gregersen
Genome Res. November 2025 35: 2550-2562; Published in Advance October 22, 2025, doi:10.1101/gr.280852.125
...-induced DNA damage (Andrade-Lima et al. 2015; Williamson et al. 2017; Cugusi et al. 2022). In addition, dysregulated transcriptional elongation has been implicated in developmental defects as well as disease and aging (Aoi and Shilatifard 2023; Debès et al. 2023).RNAPII elongation rates not only reflect...
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Research: Synergistic regulation by H3K36 and H3K27 methylation defines the chromatin landscape to control virulence and secondary metabolism in a fungal pathogen
- Xingmin Han,
- Chenghui Xu,
- Yiyi Ren,
- Meiling Guo,
- Jiayue Yan,
- Xuan Wang,
- Chao Liu,
- Qin Gu,
- Xing-Xing Shen,
- Zhonghua Ma,
- and Yun Chen
Genome Res. November 2025 35: 2472-2487; Published in Advance October 14, 2025, doi:10.1101/gr.280560.125
...regulation in eukaryotes is profoundly influenced by chromatin status, integrating diverse cellular signals to control gene expression (Berger 2007). Chromatin dynamics are modulated by multiple mechanisms, including histone modifications, DNA methylation, and chromatin remodeling complexes (Shilatifard 2006...
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Research: Genome-wide profiles of H3K9me3, H3K27me3 modifications, and DNA methylation during diapause of Asian corn borer (Ostrinia furnacalis)
- Pengfei Lv,
- Xingzhuo Yang,
- Xianguo Zhao,
- Zhangwu Zhao,
- and Juan Du
Genome Res. May 2024 34: 725-739; Published in Advance June 12, 2024, doi:10.1101/gr.278661.123
...incidence (Egi et al. 2016). Conversely, in N. vitripennis, down-regulation of DNA methyltransferases enhanced diapause (Pegoraro et al. 2016). Additionally, the expression of multiple genes regulating histone methylation and acetylation changed with diapause (Reynolds et al. 2013, 2016). In Helicoverpa...
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Research: Rtt109 slows replication speed by histone N-terminal acetylation
- Nelly Frenkel,
- Felix Jonas,
- Miri Carmi,
- Gilad Yaakov,
- and Naama Barkai
Genome Res. March 2021 31: 426-435; Published in Advance February 9, 2021, doi:10.1101/gr.266510.120
...consequences of Rtt109 activity on the H3 N-terminal acetylation remain unknown. Our study was set to examine whether this modification contributes to DNA replication dynamics.ResultsDeletion of RTT109 increases replication fork velocityHistone acetylation can reduce nucleosome stability and facilitate access...
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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...fate determinants plays a critical role in specifying these identities. Epigenetic mechanisms, such as histones and their post-translational modifications, regulate chromatin compaction, transcription, and DNA replication timing to influence cell fate decisions. In stem cells, epigenetic regulation...
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Method: Antibody-free profiling of transcription factor occupancy during early embryogenesis by FitCUT&RUN
- Xiangxiu Wang,
- Wen Wang,
- Yiman Wang,
- Jia Chen,
- Guifen Liu,
- and Yong Zhang
Genome Res. February 2022 32: 378-388; Published in Advance December 29, 2021, doi:10.1101/gr.275837.121
...). For DamID, the resolution of TF-binding sites was limited to their distribution at GATC sites, and the excessive methylation activity of the fused DNA adenine methyltransferase (Dam) may lead to false-positive enrichment (Aughey and Southall 2016). To date, only ChEC-seq applications to yeast have been...
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Research: Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts
- Yanis Zekri,
- Sebastian Gregoricchio,
- Elif Yapıcı,
- Chia-Chi Flora Huang,
- Tunç Morova,
- Umut Berkay Altıntaş,
- Gozde Korkmaz,
- Nathan A. Lack,
- and Wilbert Zwart
Genome Res. July 2025 35: 1530-1543; Published in Advance June 10, 2025, doi:10.1101/gr.280320.124
...the contribution of DNA sequence alone (Mladenova et al. 2009). However, conventional reporter assays require each regulatory sequence to be tested individually, which complicates generalizability, as the number of candidates that can be tested is limited. Recent advances in functional genomics have addressed...

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