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Method: Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates
- Marian F. Laughery,
- Bastian Stark,
- Benjamin Morledge-Hampton,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. January 2026 36: 183-196; Published in Advance December 9, 2025, doi:10.1101/gr.280384.124
...dCPD sequencing (dCPD-seq) and use it to map dCPDs across the of repair-deficient yeast cells in order to characterize the impact of DNA sequence, genomic context, and chromatin organization on CPD deamination.ResultsTo develop a method to map the deamination of cytosine-containing CPDs, we...
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Research: Genome-wide profiling reveals functional interplay of DNA sequence composition, transcriptional activity, and nucleosome positioning in driving DNA supercoiling and helix destabilization in C. elegans
- Kristina Krassovsky,
- Rajarshi P. Ghosh,
- and Barbara J. Meyer
Genome Res. July 2021 31: 1187-1202; Published in Advance June 24, 2021, doi:10.1101/gr.270082.120
...positioning and DNA sequence might play in shaping the distribution of non-B DNA. The importance of non-B DNA is well illustrated by the fact that duplex DNA in promoter regions must melt and become single-stranded for transcription to initiate. Therefore, we explored the relationship between DNA duplex...
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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...of genomic structural stability and sequence conservation than other vertebrates.Abundance and activity of transposable elements in gar sTransposable elements (TEs) are DNA sequences in the that can replicate themselves or move between chromosomes. TE activity can lead to genomic instability (Bourque et al...
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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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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...editing efficiency, we amplified genomic DNA from puromycin-selected, doubly transfected C1 cells using primers targeting regions surrounding sites recognized by sgRNAs in RE1, -2, or -3 (Supplemental Fig. S49A). PCR products were analyzed by gel electrophoresis, purified, and sequenced (Supplemental Fig...
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Method: Pangenome-based genome inference using integer programming
- Ghanshyam Chandra,
- Md Helal Hossen,
- Stephan Scholz,
- Alexander T. Dilthey,
- Daniel Gibney,
- and Chirag Jain
Genome Res. December 2025 35: 2661-2670; Published in Advance August 21, 2025, doi:10.1101/gr.280567.125
...-resolved assemblies. This graph is modeled as a DAG, in which each node is labeled with a DNA sequence, and edges represent the adjacency of these sequences along known haplotypes. Any path through this graph can represent an existing haplotype or a recombinant mosaic of segments from multiple haplotypes.In the Li...
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Mini-Review: The paradox of R-loops: guardians of the genome or drivers of disease?
- Shachinthaka D. Dissanayaka Mudiyanselage,
- Phillip Wulfridge,
- and Kavitha Sarma
Genome Res. September 2025 35: 1919-1928; Published in Advance August 6, 2025, doi:10.1101/gr.278992.124
...-rich regions. However, excessive or uncontrolled R-loop accumulation can threaten genomic stability, leading to DNA damage, particularly double-strand breaks. To preserve integrity, cells have developed mechanisms to regulate R-loop formation and resolution. Dysregulation of these processes is linked...
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Method: CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing
- Kaiyuan Zhu,
- Matthew G. Jones,
- Jens Luebeck,
- Xinxin Bu,
- Hyerim Yi,
- King L. Hung,
- Ivy Tsz-Lo Wong,
- Shu Zhang,
- Paul S. Mischel,
- Howard Y. Chang,
- and Vineet Bafna
Genome Res. September 2024 34: 1344-1354; Published in Advance July 9, 2024, doi:10.1101/gr.279131.124
...-stage cancers. ecDNAs drive tumor formation, evolution, and drug resistance by dynamically modulating oncogene copy number and rewiring gene-regulatory networks. Elucidating the genomic architecture of ecDNA amplifications is critical for understanding tumor pathology and developing more effective therapies...
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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
..., Bruhm DC, Jensen SØ, Medina JE, Hruban C, White JR, et al. 2019. Genome-wide cell-free DNA fragmentation in patients with cancer. Nature 570: 385–389. doi:10.1038/s41586-019-1272-6 ↵De Coster W, Weissensteiner MH, Sedlazeck FJ. 2021. Towards population-scale long-read sequencing. Nat Rev Genet 22: 572...
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Method: EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
- Shuyu Zhang,
- Quan Zou,
- Mengting Niu,
- Zhibin Lv,
- Antony Stalin,
- and Ximei Luo
Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
...C achieved exceptional performance on E. coli (ACC = 99.73%, AUC = 0.9999), outperforming EpiTEAmDNA by 0.67% in ACC. This represents one of the highest reported accuracy rates, surpassing 90% across all benchmark species.To ensure a statistically rigorous comparison, we conducted a side-by-side evaluation...
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