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Method: Accurate bacterial outbreak tracing with Oxford Nanopore sequencing and reduction of methylation-induced errors
- Mara Lohde,
- Gabriel E. Wagner,
- Johanna Dabernig-Heinz,
- Adrian Viehweger,
- Sascha D. Braun,
- Stefan Monecke,
- Celia Diezel,
- Claudia Stein,
- Mike Marquet,
- Ralf Ehricht,
- Mathias W. Pletz,
- and Christian Brandt
Genome Res. November 2024 34: 2039-2047; Published in Advance October 23, 2024, doi:10.1101/gr.278848.123
...). Further advances that reduce methylation-induced errors for certain specific motifs are being developed, as shown for Listeria monocytogenes and Escherichia coli (Hallgren et al. 2021; Chiou et al. 2023). Nevertheless, we strongly recommend constantly testing and evaluating reconstructed prokaryotic s...
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Research: Synergistic regulation by H3K36 and H3K27 methylation defines the chromatin landscape to control virulence and secondary metabolism in a fungal pathogen
- Xingmin Han,
- Chenghui Xu,
- Yiyi Ren,
- Meiling Guo,
- Jiayue Yan,
- Xuan Wang,
- Chao Liu,
- Qin Gu,
- Xing-Xing Shen,
- Zhonghua Ma,
- and Yun Chen
Genome Res. November 2025 35: 2472-2487; Published in Advance October 14, 2025, doi:10.1101/gr.280560.125
..., development, virulence, and stress response in F. graminearumTo determine if F. graminearum Set2 and Ash1 possess H3K36 methyltransferase activity, we heterologously expressed and purified them in Escherichia coli for in vitro enzyme assays. A recombinant H3K36 peptide, devoid of pre-existing histone...
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Research: Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains
- Stephen J. Salipante,
- David J. Roach,
- Jacob O. Kitzman,
- Matthew W. Snyder,
- Bethany Stackhouse,
- Susan M. Butler-Wu,
- Choli Lee,
- Brad T. Cookson,
- and Jay Shendure
Genome Res. January 2015 25: 119-128; Published in Advance November 4, 2014, doi:10.1101/gr.180190.114
...blood- or urine-derived isolates of extraintestinal pathogenic (ExPEC) Escherichia coli, a common agent of sepsis and community-acquired urinary tract infections, obtained during the course of routine clinical care at a single institution. We find that ExPEC E. coli are highly genomically heterogeneous...
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Method: Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe
- Arnaud Belcour,
- Jeanne Got,
- Méziane Aite,
- Ludovic Delage,
- Jonas Collén,
- Clémence Frioux,
- Catherine Leblanc,
- Simon M. Dittami,
- Samuel Blanquart,
- Gabriel V. Markov,
- and Anne Siegel
Genome Res. June 2023 33: 972-987; Published in Advance July 19, 2023, doi:10.1101/gr.277056.122
...in bacteria, metabolic and phylogenetic distances between Escherichia coli and Shigella strains could be explained by the parasitic lifestyle of the latter (Vieira et al. 2011). Another GSMN-based study of 301 s from the human gut microbiota identified marginal metabolic differences at the microbiota family...
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Research: Genome-wide promoter assembly in E. coli measured at single-base resolution
- Jordan John,
- Javaid Jabbar,
- Nitika Badjatia,
- Matthew J. Rossi,
- William K.M. Lai,
- and B. Franklin Pugh
Genome Res. May 2022 32: 878-892; Published in Advance April 28, 2022, doi:10.1101/gr.276544.121
...of the epigenomic organization of the Escherichia coli transcription machinery and nucleoid structural proteins at the time when cells are growing exponentially and upon rapid reprogramming (acute heat shock). We examined the site specificity of three sigma factors (RpoD/σ70, RpoH/σ32, and RpoN/σ54), RNA polymerase...
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Research: Large-scale genome analysis of bovine commensal Escherichia coli reveals that bovine-adapted E. coli lineages are serving as evolutionary sources of the emergence of human intestinal pathogenic strains
- Yoko Arimizu,
- Yumi Kirino,
- Mitsuhiko P. Sato,
- Koichi Uno,
- Toshio Sato,
- Yasuhiro Gotoh,
- Frédéric Auvray,
- Hubert Brugere,
- Eric Oswald,
- Jacques G. Mainil,
- Kelly S. Anklam,
- Dörte Döpfer,
- Shuji Yoshino,
- Tadasuke Ooka,
- Yasuhiro Tanizawa,
- Yasukazu Nakamura,
- Atsushi Iguchi,
- Tomoko Morita-Ishihara,
- Makoto Ohnishi,
- Koichi Akashi,
- Tetsuya Hayashi,
- and Yoshitoshi Ogura
Genome Res. September 2019 29: 1495-1505; Published in Advance August 22, 2019, doi:10.1101/gr.249268.119
...Typing: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping. Microb Genom 4. doi:10.1099/mgen.0.000192 ↵Beutin L, Geier D, Steinrück H, Zimmermann S, Scheutz F. 1993. Prevalence and some properties of verotoxin (Shiga-like toxin)-producing Escherichia coli in seven different...
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Research: Characterization of functional relationships of R-loops with gene transcription and epigenetic modifications in rice
- Yuan Fang,
- Lifen Chen,
- Kande Lin,
- Yilong Feng,
- Pengyue Zhang,
- Xiucai Pan,
- Jennifer Sanders,
- Yufeng Wu,
- Xiu-e Wang,
- Zhen Su,
- Caiyan Chen,
- Hairong Wei,
- and Wenli Zhang
Genome Res. August 2019 29: 1287-1297; Published in Advance July 1, 2019, doi:10.1101/gr.246009.118
....DNA–RNA hybrids, also referred to as R-loops, are three-stranded nucleic acid structures, and each is composed of a DNA–RNA duplex and a DNA strand displaced in a single-stranded conformation. R-loops were first found in the f1 phage in 1967 (Milman et al. 1967) and were subsequently characterized in Escherichia...
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Research: Tracing human stem cell lineage during development using DNA methylation
- Lucas A. Salas,
- John K. Wiencke,
- Devin C. Koestler,
- Ze Zhang,
- Brock C. Christensen,
- and Karl T. Kelsey
Genome Res. September 2018 28: 1285-1295; Published in Advance August 2, 2018, doi:10.1101/gr.233213.117
...reference synthetic cell mixtures by mixing cord blood and adult peripheral blood DNA methylation signatures in silico (Supplemental Table S1, synthetic mixtures data sets), varying the fraction of fetal cord blood across mixtures. Application of our algorithm to the reference synthetic cell mixtures showed...
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Method: GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens
- Zhemin Zhou,
- Nabil-Fareed Alikhan,
- Martin J. Sergeant,
- Nina Luhmann,
- Cátia Vaz,
- Alexandre P. Francisco,
- João André Carriço,
- and Mark Achtman
Genome Res. September 2018 28: 1395-1404; Published in Advance July 26, 2018, doi:10.1101/gr.232397.117
..., et al. 2011. Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology. PLoS One 6: e22751. ↵Moura A, Criscuolo A, Pouseele H, Maury MM, Leclercq A, Tarr C, Bjorkman JT, Dallman T, Reimer A, Enouf V, et al...
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Resource: Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships
- Michelle Kudron,
- Louis Gevirtzman,
- Alec Victorsen,
- Bridget C. Lear,
- Jiahao Gao,
- Jinrui Xu,
- Swapna Samanta,
- Emily Frink,
- Adri Tran-Pearson,
- Chau Huynh,
- Dionne Vafeados,
- Ann Hammonds,
- William Fisher,
- Martha Wall,
- Greg Wesseling,
- Vanessa Hernandez,
- Zhichun Lin,
- Mary Kasparian,
- Kevin White,
- Ravi Allada,
- Mark Gerstein,
- LaDeana Hillier,
- Susan E. Celniker,
- Valerie Reinke,
- and Robert H. Waterston
Genome Res. December 2024 34: 2319-2334; Published in Advance October 22, 2024, doi:10.1101/gr.279037.124
...authors: watersto@uw.edu, valerie.reinke@yale.eduAbstractA catalog of transcription factor (TF) binding sites in the is critical for deciphering regulatory relationships. Here, we present the culmination of the efforts of the modENCODE (model organism Encyclopedia of DNA Elements) and modERN (model...

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