Searching journal content for articles similar to Warren et al..

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  1. 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
    ...restriction–modification system (RM system). This system safeguards bacteria against phage and other invasive foreign DNA (O'Brown et al. 2019; Yu et al. 2021; Xiong et al. 2022). Consequently, 4mC is recognized as a key regulator of gene expression, DNA repair, and antiphage immunity in prokaryotes...
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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
    ...the QIAamp Circulating Nucleic Acid Kit (Qiagen). pUC19 was extracted from dam-/dcm- Escherichia coli cells using the Monarch Plasmid Miniprep Kit (NEB), and then 10 µg of pUC19 was CpG methylated in vitro using 40 U of M.SssI (NEB) in a 200-µL final reaction volume for 2 h at 37°C. DNA was isolated using...
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  3. Research: Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution
    • Amit Blumberg,
    • Edward J. Rice,
    • Anshul Kundaje,
    • Charles G. Danko,
    • and Dan Mishmar
    Genome Res. March 2017 27: 362-373; Published in Advance January 3, 2017, doi:10.1101/gr.209924.116
    ...responsible for transcription pausing in Escherichia coli by destabilizing bacterial RNA polymerase (Larson et al. 2014; Vvedenskaya et al. 2014). We found two such tandem motifs within the light-strand pausing peak (Fig. 3). As an alternative model, we also tested whether pausing occurs because POLRMT...
  4. LETTER: Engineering a Reduced Escherichia coli Genome
    • Vitaliy Kolisnychenko,
    • Guy Plunkett III,
    • Christopher D. Herring,
    • Tamás Fehér,
    • János Pósfai,
    • Frederick R. Blattner,
    • and György Pósfai
    Genome Res. April 1, 2002 12: 640-647; doi:10.1101/gr.217202
    .... [Sequence data described in this paper have been submitted to the DNA Data Bank of Japan, European Molecular Biology Laboratory, and GenBank databases under accession nos. AF402780 , AF402779 , and AF406953 , respectively.] Escherichia coli is both a tool and object of study of science. As the primary model...
  5. Letter: Inference of the impact of insertion sequence (IS) elements on bacterial genome diversification through analysis of small-size structural polymorphisms in Escherichia coli O157 genomes
    • Tadasuke Ooka,
    • Yoshitoshi Ogura,
    • Md Asadulghani,
    • Makoto Ohnishi,
    • Keisuke Nakayama,
    • Jun Terajima,
    • Haruo Watanabe,
    • and Tetsuya Hayashi
    Genome Res. October 2009 19: 1809-1816; Published in Advance June 29, 2009, doi:10.1101/gr.089615.108
    .... 2002. Escherichia coli insertion sequence IS150: Transposition via circular and linear intermediates. J Bacteriol 184: 5833–5841. Halling C, Calendar R, Christie GE, Dale EC, Deho G, Finkel S, Flensburg J, Ghisotti D, Kahn ML, Lane KB, et al. 1990. DNA sequence of satellite bacteriophage P4. Nucleic...
  6. RESOURCE: BAC Library of T. pallidum DNA in E. coli
    • David Šmajs,
    • Matthew McKevitt,
    • Ling Wang,
    • Jerrilyn K. Howell,
    • Steven J. Norris,
    • Timothy Palzkill,
    • and George M. Weinstock
    Genome Res. March 1, 2002 12: 515-522; doi:10.1101/gr.207302
    ...pallidum subspecies pallidum (Nichols) chromosomal DNA was used to construct a large insert bacterial artificial chromosome (BAC) library in Escherichia coli DH10B using the pBeloBAC11 cloning vector; 678 individual insert termini of 339 BAC clones (13.9 x coverage) were sequenced and the cloned...
  7. Research: Lambdoid phages with abundant Chi recombination hotspots reflect diverse viral strategies for recombination-dependent growth
    • Clarence Zheng,
    • Sherwood R. Casjens,
    • Alan R. Davidson,
    • Susan K. Amundsen,
    • and Gerald R. Smith
    Genome Res. August 2025 35: 1767-1780; Published in Advance July 10, 2025, doi:10.1101/gr.280248.124
    ...; Dillingham and Kowalczykowski 2008; Handa et al. 2012; Wigley 2013; Levy et al. 2015; Cheng et al. 2020; Millman et al. 2020; Wilkinson et al. 2022) have stated that RecBCD distinguishes E. coli’s DNA from other (“foreign”) DNA based on Chi and destroys intracellular foreign DNA while saving E. coli DNA...
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  8. LETTER: CpG dinucleotides and the mutation rate of non-CpG DNA
    • Jean-Claude Walser,
    • Loïc Ponger,
    • and Anthony V. Furano
    Genome Res. September 2008 18: 1403-1414; Published in Advance June 11, 2008, doi:10.1101/gr.076455.108
    ...during DNA replication has been demonstrated in vitro for prokaryotic DNA replication. The Escherichia coli error-prone Y family DNA polymerase pol IV can coexist in a DNA replication complex with the high-fidelity pol III polymerase ( Indiani et al. 2005 ). These studies showed that pol IV seamlessly...
  9. Research: Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes
    • Ovidiu Popa,
    • Einat Hazkani-Covo,
    • Giddy Landan,
    • William Martin,
    • and Tal Dagan
    Genome Res. April 2011 21: 599-609; Published in Advance January 26, 2011, doi:10.1101/gr.115592.110
    ..., in the comparison of a species pair, the designation of donor and recipient may yield slightly different results. These similarity measures correlate, but not strictly so, with phylogenetic classification (Supplemental Fig. S3). For example, in a comparison between Donor: Escherichia coli str. CFT073 and Recipient...
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  10. Research: Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain
    • James L. Shepherdson,
    • David M. Granas,
    • Jie Li,
    • Zara Shariff,
    • Stephen P. Plassmeyer,
    • Alex S. Holehouse,
    • Michael A. White,
    • and Barak A. Cohen
    Genome Res. October 2024 34: 1540-1552; Published in Advance September 25, 2024, doi:10.1101/gr.279415.124
    ...to cause LCA when homozygous, but only mild late-onset CoRD when heterozygous (Swaroop et al. 1999; Chen et al. 2002). Pathogenic missense variants have been identified in both the DNA-binding domain and transcriptional effector domain (Fig. 1A).View larger version: In this window In a new window Figure 1...
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