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Research: APOBEC3A drives deaminase mutagenesis in human gastric epithelium
- Yohan An,
- Ji-Hyun Lee,
- Joonoh Lim,
- Jeonghwan Youk,
- Seongyeol Park,
- Ji-Hyung Park,
- Kijong Yi,
- Taewoo Kim,
- Chang Hyun Nam,
- Won Hee Lee,
- Soo A Oh,
- Yoo Jin Bae,
- Thomas M. Klompstra,
- Haeun Lee,
- Jinju Han,
- Junehwak Lee,
- Jung Woo Park,
- Jie-Hyun Kim,
- Hyunki Kim,
- Hugo Snippert,
- Bon-Kyoung Koo,
- and Young Seok Ju
Genome Res. October 2025 35: 2158-2172; Published in Advance August 26, 2025, doi:10.1101/gr.280338.124
...APOBEC-induced DNA damage, such as replication stalling or double-strand breaks (DSBs), as previously reported (Fig. 1G,H; Supplemental Fig. S5; Burns et al. 2013; Green et al. 2016).APOBEC3A, not APOBEC3B, induces genomic mutationsTo assess the mutagenic impacts of A3A and A3B, we investigated acquired...
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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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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: Saturation mutagenesis reveals manifold determinants of exon definition
- Shengdong Ke,
- Vincent Anquetil,
- Jorge Rojas Zamalloa,
- Alisha Maity,
- Anthony Yang,
- Mauricio A. Arias,
- Sergey Kalachikov,
- James J. Russo,
- Jingyue Ju,
- and Lawrence A. Chasin
Genome Res. January 2018 28: 11-24; Published in Advance December 14, 2017, doi:10.1101/gr.219683.116
....eduAbstractTo illuminate the extent and roles of exonic sequences in the splicing of human RNA transcripts, we conducted saturation mutagenesis of a 51-nt internal exon in a three-exon minigene. All possible single and tandem dinucleotide substitutions were surveyed. Using high-throughput genetics, 5560 minigene molecules...
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Resource: Genome-scale targeted mutagenesis in Brassica napus using a pooled CRISPR library
- Jianjie He,
- Kai Zhang,
- Shuxiang Yan,
- Mi Tang,
- Weixian Zhou,
- Yongtai Yin,
- Kang Chen,
- Chunyu Zhang,
- and Maoteng Li
Genome Res. May 2023 33: 798-809; Published in Advance June 8, 2023, doi:10.1101/gr.277650.123
...@mail.hzau.edu.cn, limaoteng426@hust.edu.cnAbstractThe recently constructed mutant libraries of diploid crops by the CRISPR-Cas9 system have provided abundant resources for functional genomics and crop breeding. However, because of the complexity, it is a big challenge to accomplish large-scale targeted mutagenesis...
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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
...Mutagenesis of human s by endogenous mobile elements on a population scale Nelson T. Chuang1,2,3, Eugene J. Gardner1,2,6, Diane M. Terry1,2, Jonathan Crabtree2, Anup A. Mahurkar2, Guillermo L. Rivell4, Charles C. Hong5, James A. Perry5 and Scott E. Devine1,2,4,5 1Graduate Program in Molecular...
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Method: Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations
- Jonathan S. Brammeld,
- Mia Petljak,
- Inigo Martincorena,
- Steven P. Williams,
- Luz Garcia Alonso,
- Alba Dalmases,
- Beatriz Bellosillo,
- Carla Daniela Robles-Espinoza,
- Stacey Price,
- Syd Barthorpe,
- Patrick Tarpey,
- Constantine Alifrangis,
- Graham Bignell,
- Joana Vidal,
- Jamie Young,
- Lucy Stebbings,
- Kathryn Beal,
- Michael R. Stratton,
- Julio Saez-Rodriguez,
- Mathew Garnett,
- Clara Montagut,
- Francesco Iorio,
- and Ultan McDermott
Genome Res. April 2017 27: 613-625; Published in Advance February 8, 2017, doi:10.1101/gr.213546.116
...Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer and identification of drug resistance mutations Jonathan S. Brammeld,1 Mia Petljak,1 Inigo Martincorena,1 Steven P. Williams,1 Luz Garcia Alonso,2 Alba Dalmases,3 Beatriz Bellosillo,3 Carla Daniela Robles-Espinoza,4...
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Method: Single-cell RNA-seq analysis identifies markers of resistance to targeted BRAF inhibitors in melanoma cell populations
- Yu-Jui Ho,
- Naishitha Anaparthy,
- David Molik,
- Grinu Mathew,
- Toby Aicher,
- Ami Patel,
- James Hicks,
- and Molly Gale Hammell
Genome Res. September 2018 28: 1353-1363; Published in Advance July 30, 2018, doi:10.1101/gr.234062.117
...these methods in the case of large complex populations. We next applied the SAKE algorithms to identify drug-resistant cellular populations as human melanoma cells respond to targeted BRAF inhibitors (BRAFi). Single-cell RNA-seq data from both the Fluidigm C1 and 10x Genomics platforms were analyzed with SAKE...
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Research: Nascent RNA folding mitigates transcription-associated mutagenesis
- Xiaoshu Chen,
- Jian-Rong Yang,
- and Jianzhi Zhang
Genome Res. January 2016 26: 50-59; Published in Advance October 30, 2015, doi:10.1101/gr.195164.115
...Nascent RNA folding mitigates transcription-associated mutagenesis Xiaoshu Chen , Jian-Rong Yang and Jianzhi Zhang Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA Corresponding...
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Research: Transposon insertional mutagenesis in Saccharomyces uvarum reveals trans-acting effects influencing species-dependent essential genes
- Monica R. Sanchez,
- Celia Payen,
- Frances Cheong,
- Blake T. Hovde,
- Sarah Bissonnette,
- Adam P. Arkin,
- Jeffrey M. Skerker,
- Rachel B. Brem,
- Amy A. Caudy,
- and Maitreya J. Dunham
Genome Res. March 2019 29: 396-406; Published in Advance January 11, 2019, doi:10.1101/gr.232330.117
...-throughput experimental testing of gene dispensability in Saccharomyces uvarum, a sister species of Saccharomyces cerevisiae. We created haploid and heterozygous diploid Tn7 insertional mutagenesis libraries in S. uvarum to identify species-dependent essential genes, with the goal of detecting genes with divergent...

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