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Research: E4F1 and ZNF148 are transcriptional activators of the −57A > C and wild-type TERT promoter
- Boon Haow Chua,
- Nurkaiyisah Zaal Anuar,
- Laure Ferry,
- Cecilia Domrane,
- Anna Wittek,
- Vineeth T. Mukundan,
- Sudhakar Jha,
- Falk Butter,
- Daniel G. Tenen,
- Pierre-Antoine Defossez,
- and Dennis Kappei
Genome Res. November 2023 33: 1893-1905; Published in Advance November 2, 2023, doi:10.1101/gr.277724.123
...> T mutants only) (Li et al. 2015), as well as phosphorylated ETS1 (owing to constitutive MAPK pathway caused by NRAS/BRAF mutations in melanoma) (Vallarelli et al. 2016).View larger version: In this window In a new window Figure 1. ZNF148 and E4F1 bind to WT and −57A > C TERT promoter sequence...
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Research: Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres
- Ursula Oggenfuss,
- Robert T. Todd,
- Natthapon Soisangwan,
- Bailey Kemp,
- Alison Guyer,
- Annette Beach,
- and Anna Selmecki
Genome Res. April 2025 35: 824-838; Published in Advance October 22, 2024, doi:10.1101/gr.279301.124
...-read sequencing reveals dynamic -wide SVs in three clinical isolates. (A) Genome-wide genomic landscape: Gene content and TE content in 5000 bp windows of the C. albicans reference . Distribution of SVs in SC5314, L26, and P75063. Colors indicate the SV type in comparison with the reference : green...
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Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
- Shahmir Naseer,
- Thomas C Clark,
- Bertrand Collet,
- Pooran Dewari,
- Damir Baranasic,
- Daniel J Macqueen,
- Pierre Boudinot,
- and Samuel A.M. Martin
Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
...genes in antiviral immunity. 230 A subset of 1,348 genes (set 2 above) showed significant increases in chromatin 231 accessibility and H3K27ac signal without corresponding changes in transcript levels. To 232 further investigate this finding, we analysed the genomic context of the associated peaks. 233...
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Research: Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements
- Luis E. Valentin-Alvarado,
- Ling-Dong Shi,
- Kathryn E. Appler,
- Alexander Crits-Christoph,
- Valerie De Anda,
- Benjamin A. Adler,
- Michael L. Cui,
- Lynn Ly,
- Pedro Leão,
- Richard J. Roberts,
- Rohan Sachdeva,
- Brett J. Baker,
- David F. Savage,
- and Jillian F. Banfield
Genome Res. October 2024 34: 1595-1609; Published in Advance October 15, 2024, doi:10.1101/gr.279480.124
..., methylation pattern analysis, comparative genomics, and functional and structural prediction to explore integrated and coexisting MGEs of one group of Asgard archaea. These analyses brought to light an extensive landscape of MGEs that associate with Atabeyarchaeia, including viruses, plasmids, and as...
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Method: Enabling efficient and robust analysis of tandem repeats in genomic data using wavefront-based string decomposer
- Junhai Qi,
- Zhidong Yang,
- Ting Yu,
- and Guojun Li
Genome Res. April 8, 2026 gr.281346.125; Published in Advance April 8, 2026, doi:10.1101/gr.281346.125
..., Iafrate AJ, Letovsky S, et al.. 2011. Aberrant overexpression of364 satellite repeats in pancreatic and other epithelial cancers. Science 331: 593–596.365 Zhang P, Wei Y, Tian Q, Zou Q, and Wang Y. 2025. Fast sequence alignment for centromere with rama. Genome Research pp. gr–279763.366 Genome Res GENOME...
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Method: Automated interpretable artificial intelligence genomic prediction with AIGP
- Lei Wei,
- Ziqin Jiang,
- Baoliang Fan,
- Yidan Yan,
- Zhenqiang Xu,
- Xiaoxiang Hu,
- and Yuzhe Wang
Genome Res. April 2026 36: 814-826; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
...prediction and emphasize the importance of explainable ML approaches, integration of prior information, and parameter optimization. The AIGP toolkit enables automated model optimization and interpretability, making ML-driven genomic selection more accessible and providing new tools to support genomic...
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Method: Autoencoders for genomic variation analysis
- Margarita Geleta,
- Daniel Mas Montserrat,
- Xavier Giro-i-Nieto,
- and Alexander G. Ioannidis
Genome Res. February 2026 36: 348-360; Published in Advance January 20, 2026, doi:10.1101/gr.280086.124
..., Barcelona 08034, Spain; 3Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, California 94720, USA; 4Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95060, USA; 5Institute for Computational and Mathematical Engineering...
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Research: Adaptation of centromeres to breakage through local genomic and epigenomic remodeling in wheat
- Jingwei Zhou,
- Yuhong Huang,
- Huan Ma,
- Yiqian Chen,
- Chuanye Chen,
- Fangpu Han,
- and Handong Su
Genome Res. November 2025 35: 2461-2471; Published in Advance September 30, 2025, doi:10.1101/gr.280913.125
...for safeguarding genomic stability. Due to their intricate and fragile nature, centromeres are susceptible to chromosomal rearrangements. However, the mechanisms preserving their functional integrity and supporting nuclear homeostasis following breakages remain enigmatic. In this study, we use wheat ditelosomic...
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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
...polymerization and smooth muscle contraction. Here, we show that the genomic distribution of ACTB is SETD3-dependent and that this regulation modulates the transcription of genes involved in cell adhesion and mRNA translation in colorectal cancer cells. Proteomic analyses reveal that ACTB and SETD3 interact...
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Research: Genomic epidemiology of carbapenem-resistant Enterobacterales at a New York City hospital over a 10-year period reveals complex plasmid-clone dynamics and evidence for frequent horizontal transfer of bla_KPC
- Angela Gomez-Simmonds,
- Medini K. Annavajhala,
- Dwayne Seeram,
- Todd W. Hokunson,
- Heekuk Park,
- and Anne-Catrin Uhlemann
Genome Res. November 2024 34: 1895-1907; Published in Advance October 4, 2024, doi:10.1101/gr.279355.124
.... Overall, this points to both the continued dominance of K. pneumoniae ST258 and the dissemination of blaKPC across clones and species by diverse plasmid backbones. These findings support integrating long-read sequencing into genomic surveillance approaches to detect the hitherto silent spread...
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