Searching journal content for articles similar to John et al. 32 (5): 878.

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  1. 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
    ...-in orientations in vitro (Song et al. 2011, 2014). However, to what extent nucleosomes modulate CPD deamination in other sequence contexts and across the of intact cells remains unclear.Genome-wide sequencing methods have emerged as powerful tools to understand how different genomic and chromatin contexts impact...
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  2. Method: Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA
    • Romualdas Vaisvila,
    • V.K. Chaithanya Ponnaluri,
    • Zhiyi Sun,
    • Bradley W. Langhorst,
    • Lana Saleh,
    • Shengxi Guan,
    • Nan Dai,
    • Matthew A. Campbell,
    • Brittany S. Sexton,
    • Katherine Marks,
    • Mala Samaranayake,
    • James C. Samuelson,
    • Heidi E. Church,
    • Esta Tamanaha,
    • Ivan R. Corrêa, Jr.,
    • Sriharsa Pradhan,
    • Eileen T. Dimalanta,
    • Thomas C. Evans, Jr.,
    • Louise Williams,
    • and Theodore B. Davis
    Genome Res. July 2021 31: 1280-1289; Published in Advance June 17, 2021, doi:10.1101/gr.266551.120
    .... Dimalanta, Thomas C. Evans Jr., Louise Williams and Theodore B. Davis New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA ↵1 These authors contributed equally to this work. Corresponding author: lwilliams@neb.comAbstractBisulfite sequencing detects 5mC and 5hmC at single-base resolution...
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  3. Method: DENT-seq for genome-wide strand-specific identification of DNA single-strand break sites with single-nucleotide resolution
    • Juniper J. Elacqua,
    • Navpreet Ranu,
    • Sarah E. DiIorio,
    • and Paul C. Blainey
    Genome Res. January 2021 31: 75-87; Published in Advance December 21, 2020, doi:10.1101/gr.265223.120
    ...of the target sequence and were also adjacent to a Cas9 PAM site.View larger version: In this window In a new window Figure 5. Single-base-pair resolution detection of nicks in genomic DNA. (A) Schematic of an E. coli used to test DENT-seq, in which red arrows represent the activity of Cas9 nickase paired...
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  4. Method: Genome-wide TOP2A DNA cleavage is biased toward translocated and highly transcribed loci
    • Xiang Yu,
    • James W. Davenport,
    • Karen A. Urtishak,
    • Marie L. Carillo,
    • Sager J. Gosai,
    • Christos P. Kolaris,
    • Jo Ann W. Byl,
    • Eric F. Rappaport,
    • Neil Osheroff,
    • Brian D. Gregory,
    • and Carolyn A. Felix
    Genome Res. July 2017 27: 1238-1249; Published in Advance April 6, 2017, doi:10.1101/gr.211615.116
    ...orchestrate proper DNA topology, and they are the targets of anti-cancer drugs that cause treatment-related leukemias with balanced translocations. Here, we develop a high-throughput sequencing technology to define TOP2 cleavage sites at single-base precision, and use the technology to characterize TOP2A...
  5. Resource: A single-base resolution map of an archaeal transcriptome
    • Omri Wurtzel,
    • Rajat Sapra,
    • Feng Chen,
    • Yiwen Zhu,
    • Blake A. Simmons,
    • and Rotem Sorek
    Genome Res. January 2010 20: 133-141; Published in Advance November 2, 2009, doi:10.1101/gr.100396.109
    ...A single-base resolution map of an archaeal transcriptome Omri Wurtzel 1 , Rajat Sapra 2 , 3 , Feng Chen 4 , Yiwen Zhu 4 , 5 , Blake A. Simmons 2 , 3 and Rotem Sorek 1 , 6 1 Department of Molecular Genetics...
  6. Research: A heterozygous IDH1R132H/WT mutation induces genome-wide alterations in DNA methylation
    • Christopher G. Duncan,
    • Benjamin G. Barwick,
    • Genglin Jin,
    • Carlo Rago,
    • Priya Kapoor-Vazirani,
    • Doris R. Powell,
    • Jen-Tsan Chi,
    • Darell D. Bigner,
    • Paula M. Vertino,
    • and Hai Yan
    Genome Res. December 2012 22: 2339-2355; Published in Advance August 16, 2012, doi:10.1101/gr.132738.111
    ...A heterozygous IDH1 R132H/WT mutation induces genome-wide alterations in DNA methylation Christopher G. Duncan 1 , 6 , Benjamin G. Barwick 2 , 6 , Genglin Jin 1 , Carlo Rago 3 , Priya Kapoor-Vazirani 4 , Doris R. Powell 4...
  7. Research: Genome-wide genetic variations are highly correlated with proximal DNA methylation patterns
    • Wei Qu,
    • Shin-ichi Hashimoto,
    • Atsuko Shimada,
    • Yoichiro Nakatani,
    • Kazuki Ichikawa,
    • Taro L. Saito,
    • Katsumi Ogoshi,
    • Kouji Matsushima,
    • Yutaka Suzuki,
    • Sumio Sugano,
    • Hiroyuki Takeda,
    • and Shinichi Morishita
    Genome Res. August 2012 22: 1419-1425; Published in Advance June 11, 2012, doi:10.1101/gr.140236.112
    ...single-base resolution methylomes in two inbred medaka ( Oryzias latipes ) strains with sufficient genetic divergence (3.4%). We found that the SNP rate also increased by ∼50% ( P < 10 −2170 ), and the substitution rates in all dinucleotides increased simultaneously ( P < 10 −441 ) around...
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  8. 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
    ...-species 4mC prediction. In contrast, encoding schemes such as ANF, NAC, and TAC were not selected in most species, suggesting that their representational capabilities might be limited by specific sequence context environments.Comparison with single base modelsIn this section, we further evaluated...
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  9. Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
    • Andrew D. Bates,
    • Dawid Grzela,
    • Maciej Studzian,
    • Louise Brennan,
    • Moli Williams,
    • Conor Fawcett,
    • Beth Hammond,
    • Manreen Grewal,
    • Marcin Ratajewski,
    • Lukasz Pulaski,
    • and Urszula L. McClurg
    Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
    ...FANTOM5 (Kawaji et al. 2014) or DBTSS (Suzuki et al. 2015). However, for genes expressed at a low level, whole- experiments might not have enough coverage to reliably pinpoint TSS(s).Several databases provide comprehensive DNA methylation data derived from high-throughput sequencing, including single-base...
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  10. Resource: MPRAbase a Massively Parallel Reporter Assay database
    • Jingjing Zhao,
    • Fotis A Baltoumas,
    • Maxwell A Konnaris,
    • Ioannis Mouratidis,
    • Zhe Liu,
    • Jasmine Sims,
    • Vikram Agarwal,
    • Georgios A Pavlopoulos,
    • Ilias Georgakopoulos-Soares,
    • and Nadav Ahituv
    Genome Res. April 22, 2025 gr.280387.124; Published in Advance April 22, 2025, doi:10.1101/gr.280387.124
    .... 2019. Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution. Nat Commun 10: 3583. doi: 10.1038/s41467-019-11526-w. Klein JC, Agarwal V, Inoue F, Keith A, Martin B, Kircher M, Ahituv N, Shendure J. 2020. A systematic evaluation of the design and context...
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