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Research: Mutational signatures of DNA mismatch repair deficiency in C. elegans and human cancers
- Bettina Meier,
- Nadezda V. Volkova,
- Ye Hong,
- Pieta Schofield,
- Peter J. Campbell,
- Moritz Gerstung,
- and Anton Gartner
Genome Res. May 2018 28: 666-675; Published in Advance April 10, 2018, doi:10.1101/gr.226845.117
...to extrinsic and intrinsic mutational processes leaving behind characteristic signatures in the . DNA mismatch repair (MMR) deficiency leads to hypermutation and is found in different cancer types. Although it is possible to associate mutational signatures extracted from human cancers with possible mutational...
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Research: Age-dependent mutational loads in human tRNA genes are tumor-specific and result in chimeric tRNA sequences that could disrupt the genetic code
- Marina Murillo,
- Marina Salvadores,
- Aina Vaquer Picó,
- Lina Tsapanou,
- Adrian Gabriel Torres,
- Fran Supek,
- and Lluis Ribas de Pouplana
Genome Res. April 15, 2026 gr.281022.125; Published in Advance April 15, 2026, doi:10.1101/gr.281022.125
...efficiency and fidelity, and cause cell-specific proteostasis degeneration. Keywords: tRNAs, tDNAs, somatic mutagenesis, transcription associated mutagenesis, mutational signatures, APOBEC3, mistranslation, cancer Introduction. 1 The translational machinery of cells is finely tuned to maintain proteostasis...
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Method: Highly efficient and scarless genome editing via essential gene-coupled homology-directed repair
- Joo Hye Yeo,
- Hyongbum Henry Kim,
- Sang Ho Oh,
- and Jinu Lee
Genome Res. April 15, 2026 gr.281194.125; Published in Advance April 15, 2026, doi:10.1101/gr.281194.125
.... 50 51 INTRODUCTION 52 Homology-directed repair (HDR) is a widely used pathway for precise editing, 53 employing CRISPR–Cas9, which enables the accurate insertion or correction of specific 54 DNA sequences at defined genomic loci. HDR-mediated editing is broadly applied in 55 biomedical research...
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Research: Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans
- Jun Kim,
- Haoyu Wang,
- and Sevinç Ercan
Genome Res. May 2025 35: 1108-1123; Published in Advance April 10, 2025, doi:10.1101/gr.279365.124
...called “fountains,” which have also been reported in zebrafish and mice. These are population average reflections of DNA loops originating from distinct genomic regions and are ∼20–40 kb in C. elegans. Hi-C analysis upon cohesin and WAPL-1 depletion supports the idea that cohesin is preferentially loaded...
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Resource: A systems view on DNA damage response kinetics in Tetrahymena
- Emily Nischwitz,
- Vivien A.C. Schoonenberg,
- Rachel Mullner,
- Albert Fradera-Sola,
- Susanne Zimbelmann,
- Joshua J. Smith,
- and Falk Butter
Genome Res. January 28, 2026 ; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
...damage response transcripts. NER: nucleotide excision repair, ICL: inter crosslink repair, BER: base excision repair, DSBR: double-strand break repair, MMR:mismatch repair, DDR: DNA damage response, UV: ultraviolet light, CPT: cisplatin, HP: hydrogen peroxide, MMS: methyl methanesulfonate, IR: ionizing...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...its genetics and genomics fully reproducible by C. elegans laboratories over many years. CGC1 is available at the Caenorhabditis Genetics Center stock center (https://cgc.umn.edu/strain/CGC1).Genome sequencing and assemblyWe harvested genomic DNA (gDNA) from CGC1 and sequenced it in two sets apiece...
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Method: A full-proteome, interaction-specific characterization of mutational hotspots across human cancers
- Siwei Chen,
- Yuan Liu,
- Yingying Zhang,
- Shayne D. Wierbowski,
- Steven M. Lipkin,
- Xiaomu Wei,
- and Haiyuan Yu
Genome Res. January 2022 32: 135-149; Published in Advance December 28, 2021, doi:10.1101/gr.275437.121
...as melanoma is now delineated as BRAF-positive or BRAF-negative melanoma, a meaningful distinction with respect to therapy with BRAF and MAPK pathway inhibitors. Similarly, whether a tumor has deficient DNA mismatch repair defines whether the patient is eligible for immune checkpoint inhibitor monoclonal...
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Research: DNA mismatch repair preferentially protects genes from mutation
- Eric J. Belfield,
- Zhong Jie Ding,
- Fiona J.C. Jamieson,
- Anne M. Visscher,
- Shao Jian Zheng,
- Aziz Mithani,
- and Nicholas P. Harberd
Genome Res. January 2018 28: 66-74; Published in Advance December 12, 2017, doi:10.1101/gr.219303.116
..., Schrauwen S, Smeets D, Matthijs G, et al. 2014. Mismatch repair deficiency endows tumors with a unique mutation signature and sensitivity to DNA double-strand breaks. eLife 3: e02725. ↵Zhu YO, Siegal ML, Hall DW, Petrov DA. 2014. Precise estimates of mutation rate and spectrum in yeast. Proc Natl Acad Sci...
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Research: Endonucleolytic cleavage is the primary mechanism of decay elicited by C. elegans nonsense-mediated mRNA decay
- Marcus J. Viscardi,
- Enisha Sehgal,
- and Joshua A. Arribere
Genome Res. June 2025 35: 1337-1348; Published in Advance May 9, 2025, doi:10.1101/gr.280046.124
...results support the idea that SMG-5 and SMG-6 regulate a common set of target mRNAs with UPF1 in C. elegans, similar to findings in human cells (Boehm et al. 2021).Mutation of smg-7 had a markedly different effect and had comparatively subtle effects on the transcriptome (Fig. 1B). This result is aligned...
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Corrigendum: Corrigendum: 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. June 2025 35: 1472-1; doi:10.1101/gr.280860.125
...and apologize for any confusion this may have caused.doi: 10.1101/gr.280860.125 Published by Cold Spring Harbor Laboratory Press Corrigendum: 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...
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