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Research: Genetic inhibitors of APOBEC3B-induced mutagenesis
- Tony M. Mertz,
- Elizabeth Rice-Reynolds,
- Ly Nguyen,
- Anna Wood,
- Cameron Cordero,
- Nicholas Bray,
- Victoria Harcy,
- Rudri K. Vyas,
- Debra Mitchell,
- Kirill Lobachev,
- and Steven A. Roberts
Genome Res. September 2023 33: 1568-1581; Published in Advance August 2, 2023, doi:10.1101/gr.277430.122
....mertz@wsu.edu and steven.roberts2@wsu.edu; srober23@uvm.eduAbstractThe cytidine deaminases APOBEC3A (A3A) and APOBEC3B (A3B) are prominent mutators of human cancer s. However, tumor-specific genetic modulators of APOBEC-induced mutagenesis are poorly defined. Here, we used a screen to identify 61 gene deletions...
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Research: Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer
- Milad Razavi-Mohseni,
- Weitai Huang,
- Yu A. Guo,
- Dustin Shigaki,
- Shamaine Wei Ting Ho,
- Patrick Tan,
- Anders J. Skanderup,
- and Michael A. Beer
Genome Res. May 2024 34: 680-695; Published in Advance May 22, 2024, doi:10.1101/gr.278565.123
...trained on accessibility and single-cell transcriptional profiles.ResultsSequence-based machine learning model of ATAC-seq profiles identifies distinct regulatory programs driving GC heterogeneityTo understand differences in epigenomic state profiles in gastric-cancer derived cell lines, we generated ATAC...
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Research: Polycomb misregulation in enterocytes drives tissue decline in the aging Drosophila intestine
- Sarah M. Leichter,
- Kami Ahmad,
- and Steven Henikoff
Genome Res. January 2026 36: 102-114; Published in Advance November 17, 2025, doi:10.1101/gr.281058.125
...: In this window In a new window Figure 6. Model for cell type–specific Polycomb remodeling drives gut aging. (A) Young gut: The epithelium is composed primarily of enterocytes, with a small population of ISC/EBs. In enterocytes, Polycomb (Pc) binds chitin-related promoters (e.g., Chs2, Cht cluster), but H3K27me3...
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Method: High-throughput and genome-scale targeted mutagenesis using CRISPR in a nonmodel multicellular organism, Bombyx mori
- Sanyuan Ma,
- Tong Zhang,
- Ruolin Wang,
- Pan Wang,
- Yue Liu,
- Jiasong Chang,
- Aoming Wang,
- Xinhui Lan,
- Le Sun,
- Hao Sun,
- Run Shi,
- Wei Lu,
- Dan Liu,
- Na Zhang,
- Wenbo Hu,
- Xiaogang Wang,
- Weiqing Xing,
- Ling Jia,
- and Qingyou Xia
Genome Res. January 2024 34: 134-144; Published in Advance January 8, 2024, doi:10.1101/gr.278297.123
...High-throughput and -scale targeted mutagenesis using CRISPR in a nonmodel multicellular organism, Bombyx mori Sanyuan Ma1, Tong Zhang1, Ruolin Wang1, Pan Wang1, Yue Liu1,2, Jiasong Chang1,3, Aoming Wang1, Xinhui Lan1, Le Sun1, Hao Sun1, Run Shi1, Wei Lu1, Dan Liu1, Na Zhang1, Wenbo Hu1, Xiaogang...
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Corrigendum: Corrigendum: Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer
- Milad Razavi-Mohseni,
- Weitai Huang,
- Yu A. Guo,
- Dustin Shigaki,
- Shamaine Wei Ting Ho,
- Patrick Tan,
- Anders J. Skanderup,
- and Michael A. Beer
Genome Res. February 2026 36: 432; doi:10.1101/gr.281294.125
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Method: Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
- Aayush Grover,
- Till Muser,
- Liine Kasak,
- Lin Zhang,
- Ekaterina Krymova,
- and Valentina Boeva
Genome Res. March 2026 36: 619-629; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125
..., or attention mechanisms, drive performance in these high-resolution predictions. To address these knowledge gaps, we systematically evaluate classic architectural choices and introduce ConvNeXt V2 blocks, originally developed for computer vision, as high-resolution feature extractors in deep learning models...
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Research: Oxidative stress accelerates intestinal tumorigenesis by enhancing 8-oxoguanine-mediated mutagenesis in MUTYH-deficient mice
- Mizuki Ohno,
- Noriko Takano,
- Kyoko Hidaka,
- Fumiko Sasaki,
- Kazumi Yamauchi,
- Yasunobu Aoki,
- Takehiko Nohmi,
- Yusaku Nakabeppu,
- Yoshimichi Nakatsu,
- and Teruhisa Tsuzuki
Genome Res. January 2024 34: 47-56; Published in Advance January 30, 2024, doi:10.1101/gr.278326.123
...Studies, Tsukuba, Ibaraki 305-8506, Japan; 5Division of Genetics and Mutagenesis, National Institute of Health Sciences, Kawasaki, Kanagawa 210-9501, Japan; 6Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka...
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Research: APOBEC3A/B-induced mutagenesis is responsible for 20% of heritable mutations in the TpCpW context
- Vladimir B. Seplyarskiy,
- Maria A. Andrianova,
- and Georgii A. Bazykin
Genome Res. February 2017 27: 175-184; Published in Advance December 9, 2016, doi:10.1101/gr.210336.116
...and Technology, Skolkovo 143026, Russia Corresponding author: alicodendrochit@gmail.com Abstract APOBEC3A/B cytidine deaminase is responsible for the majority of cancerous mutations in a large fraction of cancer samples. However, its role in heritable mutagenesis remains very poorly...
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Research: Mutagenesis of human genomes by endogenous mobile elements on a population scale
- Nelson T. Chuang,
- Eugene J. Gardner,
- Diane M. Terry,
- Jonathan Crabtree,
- Anup A. Mahurkar,
- Guillermo L. Rivell,
- Charles C. Hong,
- James A. Perry,
- and Scott E. Devine
Genome Res. December 2021 31: 2225-2235; Published in Advance November 12, 2021, doi:10.1101/gr.275323.121
...,350 nonredundant MEIs. We leveraged this collection (1) to examine potentially active L1 source elements that drive the mobilization of new Alu, L1, and SVA MEIs in humans; (2) to examine the population distributions and subfamilies of these MEIs; and (3) to examine the mutagenesis of GENCODE genes, ENCODE...
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Research: Alternative polyadenylation drives oncogenic gene expression in pancreatic ductal adenocarcinoma
- Swati Venkat,
- Arwen A. Tisdale,
- Johann R. Schwarz,
- Abdulrahman A. Alahmari,
- H. Carlo Maurer,
- Kenneth P. Olive,
- Kevin H. Eng,
- and Michael E. Feigin
Genome Res. March 2020 30: 347-360; Published in Advance February 6, 2020, doi:10.1101/gr.257550.119
..., TP53, SMAD4, CDKN2A) and dysregulated pathways (axon guidance, cell adhesion, small GTPase signaling, protein metabolism) driving disease initiation and progression (Jones et al. 2008; Waddell et al. 2015; The Cancer Genome Atlas Research Network 2017). Gene expression profiles from hundreds...
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