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Method: Global mapping of RNA homodimers in living cells
- Marta M. Gabryelska,
- Andrew P. Badrock,
- Jian You Lau,
- Raymond T. O'Keefe,
- Yanick J. Crow,
- and Grzegorz Kudla
Genome Res. May 2022 32: 956-967; Published in Advance March 24, 2022, doi:10.1101/gr.275900.121
...and computational protocols for mapping of homodimers, and globally profile the homodimerization of RNA in yeast and human cells and in Zika and SARS-CoV-2 viruses.ResultsOverlapping chimeras indicate intermolecular interactionsCLASH, PARIS, and other RNA proximity ligation methods rely on the ligation...
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Research: Global loss of cellular m⁶A RNA methylation following infection with different SARS-CoV-2 variants
- Roshan Vaid,
- Akram Mendez,
- Ketan Thombare,
- Rebeca Burgos-Panadero,
- Rémy Robinot,
- Barbara F. Fonseca,
- Nikhil R. Gandasi,
- Johan Ringlander,
- Mohammad Hassan Baig,
- Jae-June Dong,
- Jae Yong Cho,
- Björn Reinius,
- Lisa A. Chakrabarti,
- Kristina Nystrom,
- and Tanmoy Mondal
Genome Res. March 2023 33: 299-313; Published in Advance March 1, 2023, doi:10.1101/gr.276407.121
...%–95% of infected cells for all the variants (Supplemental Fig. S1A). We isolated total RNA 48 h postinfection and evaluated gene expression changes using RNA sequencing (RNA-seq). We first checked viral RNA levels postinfection and observed that RNA-seq reads mapping to the viral were comparable for the three SARS...
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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
...Large-scale 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 Arimizu1,2, Yumi Kirino3, Mitsuhiko P. Sato1, Koichi Uno4, Toshio Sato4, Yasuhiro Gotoh1, Frédéric...
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Method: Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome
- Elisa Oberbeckmann,
- Michael Wolff,
- Nils Krietenstein,
- Mark Heron,
- Jessica L. Ellins,
- Andrea Schmid,
- Stefan Krebs,
- Helmut Blum,
- Ulrich Gerland,
- and Philipp Korber
Genome Res. December 2019 29: 1996-2009; Published in Advance November 6, 2019, doi:10.1101/gr.253419.119
...occupancy, we globally rescaled their signal to have the same genomic mean as the absolute occupancy map. Here and in following cases, nucleosome dyads of external data sets were extended to 147 bp. (C) Histogram of absolute occupancy at nucleosome positions called from the indicated data sets.We measured...
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Research: Global fitness landscapes of the Shine-Dalgarno sequence
- Syue-Ting Kuo,
- Ruey-Lin Jahn,
- Yuan-Ju Cheng,
- Yi-Lan Chen,
- Yun-Ju Lee,
- Florian Hollfelder,
- Jin-Der Wen,
- and Hsin-Hung David Chou
Genome Res. May 2020 30: 711-723; Published in Advance May 18, 2020, doi:10.1101/gr.260182.119
...great sequence diversity, questioning how SD functions. Here, we determined the molecular fitness (i.e., translation efficiency) of 49 synthetic 9-nt SD genotypes in three distinct mRNA contexts in Escherichia coli. We uncovered generic principles governing the SD fitness landscapes: (1) Guanine...
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Research: Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131
- Teemu Kallonen,
- Hayley J. Brodrick,
- Simon R. Harris,
- Jukka Corander,
- Nicholas M. Brown,
- Veronique Martin,
- Sharon J. Peacock,
- and Julian Parkhill
Genome Res. August 2017 27: 1437-1449; Published in Advance July 18, 2017, doi:10.1101/gr.216606.116
...2 0QQ, United Kingdom; 6Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, United Kingdom; 7British Society of Antimicrobial Chemotherapy, Birmingham B1 3NJ, United Kingdom; 8London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom Escherichia coli...
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Resource: Global analysis of protein homomerization in Saccharomyces cerevisiae
- Yeonsoo Kim,
- Jong Pil Jung,
- Chan-Gi Pack,
- and Won-Ki Huh
Genome Res. January 2019 29: 135-145; Published in Advance December 19, 2018, doi:10.1101/gr.231860.117
..., cells can build up large protein complexes by homomerization with a relatively small number of genes (Goodsell and Olson 2000). Third, proteins can go through functional transitions depending on their homomeric states. For example, Escherichia coli UvrD acts as either a helicase or a translocase...
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Resource: The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity
- Zhemin Zhou,
- Nabil-Fareed Alikhan,
- Khaled Mohamed,
- Yulei Fan,
- the Agama Study Group,
- and Mark Achtman
Genome Res. January 2020 30: 138-152; Published in Advance December 6, 2019, doi:10.1101/gr.251678.119
...://github.com/zheminzhou/EToKi) of useful modules (Supplemental Fig. S2B–E) that facilitate genomic assemblies (EToKi modules prepare and assemble), MLST (MLSType), calling nonrepetitive SNPs against a reference (EToKi modules align and phylo), or predicting serotypes of Escherichia coli from assemblies (EBEis).EnteroBase performs daily...
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Review: De novo gene birth and the conundrum of ORFan genes in bacteria
- Md. Hassan uz-Zaman and
- Howard Ochman
Genome Res. August 2025 35: 1679-1688; Published in Advance July 10, 2025, doi:10.1101/gr.280157.124
...of novel expression and its causative regulatory sequences can be identified across short evolutionary timescales. Working with the Escherichia coli Long-Term Evolution Experiment (Lenski et al. 1991; Tenaillon et al. 2016; Good et al. 2017), a system in which the ancestral states of all s and each new...

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