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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
...residues in the SARS-CoV-2 RNA . In these experiments, viral genomic RNA was isolated from infected Vero cell supernatant, and the ratio of A/m6A was measured using a synthetic m6A-containing RNA oligo as a standard. Using the parallel reaction-monitoring (PRM) mode, we monitored LC-MS/MS profiles for m...
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Research: The mode of expression divergence in Drosophila fat body is infection-specific
- Bryan A. Ramirez-Corona,
- Stephanie Fruth,
- Oluchi Ofoegbu,
- and Zeba Wunderlich
Genome Res. June 2021 31: 1024-1034; Published in Advance April 15, 2021, doi:10.1101/gr.269597.120
....MethodsAnimal genotypes, infection protocols, and survival analysisThe A4 and B6 D. melanogaster lines, SNP tables, and genomic reads were received from the Drosophila Synthetic Population Resource (King et al. 2012). Flies were reared at 25°C on standard cornmeal fly food (Brent and Oster 1974). For all RNA...
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Research: Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection–related chromatin reorganization
- Cyril Matthey-Doret,
- Morgan J. Colp,
- Pedro Escoll,
- Agnès Thierry,
- Pierrick Moreau,
- Bruce Curtis,
- Tobias Sahr,
- Matt Sarrasin,
- Michael W. Gray,
- B. Franz Lang,
- John M. Archibald,
- Carmen Buchrieser,
- and Romain Koszul
Genome Res. September 2022 32: 1698-1710; Published in Advance September 15, 2022, doi:10.1101/gr.276375.121
...relevant GO terms at the sites of these infection-induced modifications, many of which correspond to known biological processes induced by L. pneumophila in amoebae and macrophages. Several enriched terms are related to cell cycle regulation, including mitotic cell cycle, cell cycle processes, and cell...
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Method: Cancer-associated dynamics and potential regulators of intronic polyadenylation revealed by IPAFinder using standard RNA-seq data
- Zhaozhao Zhao,
- Qiushi Xu,
- Ran Wei,
- Weixu Wang,
- Dong Ding,
- Yu Yang,
- Jun Yao,
- Liye Zhang,
- Yue-Qing Hu,
- Gang Wei,
- and Ting Ni
Genome Res. November 2021 31: 2095-2106; Published in Advance September 2, 2021, doi:10.1101/gr.271627.120
...importance for further evaluating its biological significance. Here, we developed IPAFinder, a bioinformatic method for the de novo identification of intronic poly(A) sites and their dynamic changes from standard RNA-seq data. Applying IPAFinder to 256 pan-cancer tumor/normal pairs across six tumor types, we...
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Research: Genome specialization and decay of the strangles pathogen, Streptococcus equi, is driven by persistent infection
- Simon R. Harris,
- Carl Robinson,
- Karen F. Steward,
- Katy S. Webb,
- Romain Paillot,
- Julian Parkhill,
- Matthew T.G. Holden,
- and Andrew S. Waller
Genome Res. September 2015 25: 1360-1371; Published in Advance July 9, 2015, doi:10.1101/gr.189803.115
...to mutate and decay, but also to amplify and acquire genes despite the organism having lost its natural competence and become host-restricted. The lifestyle of S. equi within the horse is defined by short-term acute disease, strangles, followed by long-term infection. Population analysis reveals evidence...
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Research: Systems analysis reveals complex biological processes during virus infection fate decisions
- Jordi Argilaguet,
- Mireia Pedragosa,
- Anna Esteve-Codina,
- Graciela Riera,
- Enric Vidal,
- Cristina Peligero-Cruz,
- Valentina Casella,
- David Andreu,
- Tsuneyasu Kaisho,
- Gennady Bocharov,
- Burkhard Ludewig,
- Simon Heath,
- and Andreas Meyerhans
Genome Res. June 2019 29: 907-919; Published in Advance May 28, 2019, doi:10.1101/gr.241372.118
...-resolved splenic transcriptomes. First, we found an early attenuation of inflammatory monocyte/macrophage prior to the onset of T cell exhaustion, and second, a critical role of the XCL1-XCR1 communication axis during the functional adaptation of the T cell response to the chronic infection state. These findings...
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Research: Genome-wide chromatin interaction profiling reveals a vital role of super-enhancers and rearrangements in host enhancer contacts during BmNPV infection
- Shudi Zhao,
- Yuedong Li,
- Guanping Chen,
- Xingyang Wang,
- Nan Chen,
- and Xiaofeng Wu
Genome Res. November 2023 33: 1958-1974; Published in Advance October 23, 2023, doi:10.1101/gr.277931.123
...-enhancers with a role in regulating the expression of vital genes related to cell state maintenance through a sophisticated interaction network. Additionally, a radical attenuation of chromatin interactions is found after infection of Bombyx mori nucleopolyhedrovirus (BmNPV), the main pathogen of silkworm, which...
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Research: Collaborative Cross mice and their power to map host susceptibility to Aspergillus fumigatus infection
- Caroline Durrant,
- Hanna Tayem,
- Binnaz Yalcin,
- James Cleak,
- Leo Goodstadt,
- Fernando Pardo-Manuel de Villena,
- Richard Mott,
- and Fuad A. Iraqi
Genome Res. August 2011 21: 1239-1248; Published in Advance April 14, 2011, doi:10.1101/gr.118786.110
.... 2007. A sequencebased variationmapof 8.27million SNPs in inbredmouse strains.Nature 448: 1050–1053. Gervais F, Stevenson M, Skamene E. 1984. Genetic control of resistance to Listeria monocytogenes: regulation of leukocyte inflammatory responses by the Hc locus. J Immunol 132: 2078–2083. Grubb SC...
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Research: Bacterial infection remodels the DNA methylation landscape of human dendritic cells
- Alain Pacis,
- Ludovic Tailleux,
- Alexander M. Morin,
- John Lambourne,
- Julia L. MacIsaac,
- Vania Yotova,
- Anne Dumaine,
- Anne Danckaert,
- Francesca Luca,
- Jean-Christophe Grenier,
- Kasper D. Hansen,
- Brigitte Gicquel,
- Miao Yu,
- Athma Pai,
- Chuan He,
- Jenny Tung,
- Tomi Pastinen,
- Michael S. Kobor,
- Roger Pique-Regi,
- Yoav Gilad,
- and Luis B. Barreiro
Genome Res. December 2015 25: 1801-1811; Published in Advance September 21, 2015, doi:10.1101/gr.192005.115
...present in infected DCs resembles recent findings showing that, in response to different immune stimuli, mouse macrophages can gain de novo putative enhancer regions that were absent in naive cells (Kaikkonen et al. 2013; Ostuni et al. 2013). Interestingly, we observed that 5hmCwas significantly enriched...
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Resource: Phenotypic diversity and genotypic flexibility of Burkholderia cenocepacia during long-term chronic infection of cystic fibrosis lungs
- Amy Huei-Yi Lee,
- Stephane Flibotte,
- Sunita Sinha,
- Adrianna Paiero,
- Rachel L. Ehrlich,
- Sergey Balashov,
- Garth D. Ehrlich,
- James E.A. Zlosnik,
- Joshua Chang Mell,
- and Corey Nislow
Genome Res. April 2017 27: 650-662; Published in Advance March 21, 2017, doi:10.1101/gr.213363.116
..., acute virulence, and growth rate. These findings may be useful for clinical microbiologists in associating potential virulence traits with standard molecular diagnostic testing. Previous genotyping methods suggested that chronic B. cenocepacia infections in CF patients result from the colonization...
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