Searching journal content for articles similar to Zhu et al. 28 (7): 1067.

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  1. Method: Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications
    • Xudong Liu,
    • Ying Ni,
    • Lianwei Ye,
    • Zhihao Guo,
    • Lu Tan,
    • Jun Li,
    • Mengsu Yang,
    • Sheng Chen,
    • and Runsheng Li
    Genome Res. November 2024 34: 2025-2038; Published in Advance October 2, 2024, doi:10.1101/gr.279012.124
    ...differ in distribution and function in bacteria, but all play pivotal roles in bacterial life processes. Long-read sequencing platforms, including PacBio single-molecule real-time (SMRT) sequencing and Oxford Nanopore Technology (ONT) sequencing, have enabled the direct detection of DNA modifications...
  2. Research: Semiconservative transmission of DNA N6-adenine methylation in a unicellular eukaryote
    • Yalan Sheng,
    • Yuanyuan Wang,
    • Wentao Yang,
    • Xue Qing Wang,
    • Jiuwei Lu,
    • Bo Pan,
    • Bei Nan,
    • Yongqiang Liu,
    • Fei Ye,
    • Chun Li,
    • Jikui Song,
    • Yali Dou,
    • Shan Gao,
    • and Yifan Liu
    Genome Res. May 2024 34: 740-756; Published in Advance May 14, 2024, doi:10.1101/gr.277843.123
    ...A transmission mechanism remains to be elucidated. Taking advantage of single-molecule real-time circular consensus sequencing (SMRT CCS), here we provide definitive evidence for semiconservative transmission of 6mA in Tetrahymena thermophila. In wild-type (WT) cells, 6mA occurs at the self-complementary Ap...
  3. Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
    • Medhat Mahmoud,
    • Daniel P. Agustinho,
    • and Fritz J. Sedlazeck
    Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
    ...of the DNA (such as bisulfite sequencing). The presence of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC, ONT only) at CpG sites is recorded during the basecalling process. Other modifications, such as N6-methyladenine (6mA), can also be detected using specific contexts or methods (Kong et al...
  4. Method: DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools
    • Anupama Jha,
    • Stephanie C. Bohaczuk,
    • Yizi Mao,
    • Jane Ranchalis,
    • Benjamin J. Mallory,
    • Alan T. Min,
    • Morgan O. Hamm,
    • Elliott Swanson,
    • Danilo Dubocanin,
    • Connor Finkbeiner,
    • Tony Li,
    • Dale Whittington,
    • William Stafford Noble,
    • Andrew B. Stergachis,
    • and Mitchell R. Vollger
    Genome Res. November 2024 34: 1976-1986; Published in Advance June 7, 2024, doi:10.1101/gr.279095.124
    ...-nucleotide resolution. Long-read epigenetic studies encompass both the direct identification of native cytosine methylation and the identification of exogenously placed DNA N6-methyladenine (DNA-m6A). However, detecting DNA-m6A modifications using single-molecule sequencing, as well as coprocessing single-molecule...
  5. Research: Dynamic DNA N6-adenine methylation (6mA) governs the encystment process, showcased in the unicellular eukaryote Pseudocohnilembus persalinus
    • Yongqiang Liu,
    • Junhua Niu,
    • Fei Ye,
    • Therese Solberg,
    • Borong Lu,
    • Chundi Wang,
    • Mariusz Nowacki,
    • and Shan Gao
    Genome Res. February 2024 34: 256-271; Published in Advance March 12, 2024, doi:10.1101/gr.278796.123
    ..., which can be easily induced to form cysts to investigate the dynamic pattern of 6mA in trophonts and cysts. Single-molecule real-time (SMRT) sequencing reveals high levels of 6mA in trophonts that decrease in cysts, along with a conversion of symmetric 6mA to asymmetric 6mA. Further analysis shows...
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