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Advantages of mixing bioinformatics and visualization approaches for analyzing sRNA-mediated regulatory bacterial networks

Patricia Thébault, Romain Bourqui, William Benchimol, Christine Gaspin, Pascal Sirand-Pugnet, Raluca Uricaru, Isabelle Dutour
2014 Briefings in Bioinformatics  
In this perspective, this review aims at presenting the advantages of mixing bioinformatics and visualization approaches for analyzing predicted sRNA-mediated regulatory bacterial networks.  ...  Ongoing exploitation of these data enables numerous applications for investigating bacterial transacting sRNA-mediated regulation networks.  ...  This example illustrates the advantages of coupling bioinformatics and visualization approaches.  ... 
doi:10.1093/bib/bbu045 pmid:25477348 pmcid:PMC4570199 fatcat:g4rxhjivpjgrjghna2tdx34ooy

Regulation by Small RNAs in Bacteria: Expanding Frontiers

Gisela Storz, Jörg Vogel, Karen M. Wassarman
2011 Molecular Cell  
Current work also has begun to illuminate how sRNAs modulate expression of distinct regulons and key transcription factors, thus integrating sRNA activity into extensive regulatory networks.  ...  Most importantly, recent studies have served to clarify the abundance of remaining questions about how, when, and why sRNA-mediated regulation is of such importance to bacterial lifestyles.  ...  Fö rstner for help with Figure 3 , many colleagues for their comments, and the participants of the 2011 ASM Conference on Regulating with RNA in Bacteria for discussion, which stimulated many of the ideas  ... 
doi:10.1016/j.molcel.2011.08.022 pmid:21925377 pmcid:PMC3176440 fatcat:egfmxbkt65ekbg35ab6x6efi7q

Identification of small RNAs in Mycobacterium smegmatis using heterologous Hfq

S.-K. Li, P. K.-S. Ng, H. Qin, J. K.-Y. Lau, J. P.-Y. Lau, S. K.-W. Tsui, T.-F. Chan, T. C.-K. Lau
2012 RNA: A publication of the RNA Society  
Moreover, this novel method of using heterologous Hfq for sRNAs enrichment can be of general use for the discovery of bacterial sRNAs in which no endogenous Hfq is identified.  ...  We believe that our findings will serve as an important reference for future analysis of sRNAs regulation in mycobacteria and will contribute significantly to the development of sRNAs prediction programs  ...  of sRNAs networking and sRNAs-mediated gene regulation in mycobacteria.  ... 
doi:10.1261/rna.034116.112 pmid:23169799 pmcid:PMC3527728 fatcat:vui7abrejvepdpz3ugnx6qjwra

Transcriptomic Profiling of Yersinia pseudotuberculosis Reveals Reprogramming of the Crp Regulon by Temperature and Uncovers Crp as a Master Regulator of Small RNAs

Aaron M. Nuss, Ann Kathrin Heroven, Barbara Waldmann, Jan Reinkensmeier, Michael Jarek, Michael Beckstette, Petra Dersch, Cynthia M. Sharma
2015 PLoS Genetics  
of Yersinia fitness and virulence to the requirements of their environmental and virulent life-styles. regulatory networks which adjust synthesis of the large repertoire of crucial virulence factors and  ...  This finding highlights a novel level of complexity of the regulatory network in which the concerted action of transcriptional regulators and multiple non-coding RNAs under control of CRP adjusts the control  ...  Fenner for helpful discussions. We also thank T. Krause, M. Schoof and Y. Dzäbel for technical assistance. Author Contributions  ... 
doi:10.1371/journal.pgen.1005087 pmid:25816203 pmcid:PMC4376681 fatcat:zdhpyjf5v5eqto4dertvhemdla

smartPARE: An R Package for Efficient Identification of True mRNA Cleavage Sites

Kristian Persson Hodén, Xinyi Hu, German Martinez, Christina Dixelius
2021 International Journal of Molecular Sciences  
We conclude that our new analytic approach is useful for anyone working on complex biological systems and with the interest of identifying cleavage sites particularly inferred by sRNA classes beyond miRNAs  ...  Multiple targets and several cases of complex regulatory cascades, particularly in potato, was revealed.  ...  Acknowledgments: We thank Anna Törnkvist for help with work on the transgenic 35S:StAGO1a-GFP potato plants. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/ijms22084267 pmid:33924042 fatcat:ep6xtvgoe5atjegrfahiguswx4

A Novel Mechanism of Host-Pathogen Interaction through sRNA in Bacterial Outer Membrane Vesicles

Katja Koeppen, Thomas H. Hampton, Michael Jarek, Maren Scharfe, Scott A. Gerber, Daniel W. Mielcarz, Elora G. Demers, Emily L. Dolben, John H. Hammond, Deborah A. Hogan, Bruce A. Stanton, Marvin Whiteley
2016 PLoS Pathogens  
Bacterial outer membrane vesicle (OMV)-mediated delivery of proteins to host cells is an important mechanism of host-pathogen communication.  ...  In this study we demonstrate a novel mechanism of pathogen-host interaction that attenuates the innate immune response in human airway epithelial cells and in mouse lung through a regulatory sRNA contained  ...  For performance of the mouse multiplex cytokine assay we thank DartLab: Immunoassay and Flow Cytometry Shared Resource at the Geisel School of Medicine at Dartmouth. Author Contributions  ... 
doi:10.1371/journal.ppat.1005672 pmid:27295279 pmcid:PMC4905634 fatcat:6gpnypy6mvapxg6js4iyxfvp6m

In silico prediction and validation of potential gene targets for pospiviroid-derived small RNAs during tomato infection

Katia Avina-Padilla, Octavio Martinez de la Vega, Rafael Rivera-Bustamante, Juan Pablo Martinez-Soriano, Robert A. Owens, Rosemarie W. Hammond, Jean-Philippe Vielle-Calzada
2015 Gene  
A pool of sequence homologies among 29 species of the Pospiviroidae family and the Arabidopsis genome was analyzed.  ...  Our approach proved to be useful for the identification of natural host genes containing sequence homologies with segments of the Pospiviroidae genome.  ...  Wei Wei, Jonathan Shao, and John C. Hammond for their assistance with figures and data processing. We thank Dr. John Hammond (USDA ARS) for his critical reading of the manuscript.  ... 
doi:10.1016/j.gene.2015.03.076 pmid:25862922 fatcat:uaqbnbqcmreezkioaiyxn77npa

Identification of a Novel Small Non-Coding RNA Modulating the Intracellular Survival of Brucella melitensis

Yufei Wang, Yuehua Ke, Jie Xu, Ligui Wang, Tongkun Wang, Hui Liang, Wei Zhang, Chunli Gong, Jiuyun Yuan, Yubin Zhuang, Chang An, Shuangshuang Lei (+7 others)
2015 Frontiers in Microbiology  
In this study, by using a combined bioinformatic and experimental approach, eight novel sRNA genes were identified in intracellular pathogen Brucella melitensis.  ...  Bacterial small non-coding RNAs (sRNAs) are gene expression modulators respond to environmental changes, stressful conditions, and pathogenesis.  ...  In summary, we have identified a novel sRNA BSR0602 modulating B. melitensis intracellular survival and this provide significant insights for unraveling the sRNA-mediated regulatory networks in B. melitensis  ... 
doi:10.3389/fmicb.2015.00164 pmid:25852653 pmcid:PMC4365724 fatcat:z6lgwmrsdjho3dfph73fc6ipxm

Regulatory sRNAs in Cyanobacteria

Jinlu Hu, Qiang Wang
2018 Frontiers in Microbiology  
In this article, by focusing on cyanobacterial sRNAs, the approaches for detection and targeting of sRNAs will be summarized, four major mechanisms and regulatory functions will be generalized, eight types  ...  of cis-encoded sRNA and four types of trans-encoded sRNAs will be reviewed in detail, and their possible physiological functions will be further discussed.  ...  PROSPECT In recent years, approaches for sRNAs detecting and targeting have become a standard method used to search for several types of sRNA genes within bacterial genomes.  ... 
doi:10.3389/fmicb.2018.02399 pmid:30405542 pmcid:PMC6202907 fatcat:ncrh27q6end2hew6qx7altkpjq

Comparative Profiling of Pseudomonas aeruginosa Strains Reveals Differential Expression of Novel Unique and Conserved Small RNAs

Silvia Ferrara, Margherita Brugnoli, Angela De Bonis, Francesco Righetti, Francesco Delvillani, Gianni Dehò, David Horner, Federica Briani, Giovanni Bertoni, Pierre Cornelis
2012 PLoS ONE  
In this study, we used a deep-sequencing approach to explore the complement of small RNAs (sRNAs) in P. aeruginosa as the number of such regulatory molecules previously identified in this organism is relatively  ...  Altogether, we have identified more than 150 novel candidate sRNAs and validated a third of them by Northern blotting.  ...  Acknowledgments The authors acknowledge all members of the lab for helpful discussion and technical support, F. Dal Pero and A. Albiero for 454-pyrosequencing and data analysis, respectively, and G.  ... 
doi:10.1371/journal.pone.0036553 pmid:22590564 pmcid:PMC3349714 fatcat:te6l6z5au5aqnfbxsuurugbahu

Comparative genomics boosts target prediction for bacterial small RNAs

P. R. Wright, A. S. Richter, K. Papenfort, M. Mann, J. Vogel, W. R. Hess, R. Backofen, J. Georg
2013 Proceedings of the National Academy of Sciences of the United States of America  
a unique approach (CopraRNA, for Comparative Prediction Algorithm for sRNA Targets) towards reliably predicting the targets of bacterial small regulatory RNAs (sRNAs).  ...  The method is superior to existing bioinformatics tools (Fig. 1B) and works for a wide range of bacterial organisms.  ...  The source code for CopraRNA is available from our Software page.  ... 
doi:10.1073/pnas.1303248110 pmid:23980183 pmcid:PMC3773804 fatcat:bj3sxocbirgk3ogonc4pr3xpsm

A Stress-Induced Small RNA Modulates Alpha-Rhizobial Cell Cycle Progression

Marta Robledo, Benjamin Frage, Patrick R. Wright, Anke Becker, Patrick H. Viollier
2015 PLoS Genetics  
Post-transcriptional repression of the cell cycle key regulatory genes gcrA and dnaA mediated by mRNA base-pairing with the strongly conserved loop 1 of EcpR1 was experimentally confirmed by two-plasmid  ...  differential gene expression assays and compensatory changes in sRNA and mRNA.  ...  Acknowledgments We thank Barbara Herte and Andreas Kautz for technical assistance in the transcriptome studies, Matthew McIntosh for providing plasmid pPHUtrap and design of the sinR-P sinI indirect overexpression  ... 
doi:10.1371/journal.pgen.1005153 pmid:25923724 pmcid:PMC4414408 fatcat:7uuzdpqdkfbfhgcbevsewvabba

Genome-Wide Identification of Regulatory RNAs in the Human Pathogen Clostridium difficile

Olga A. Soutourina, Marc Monot, Pierre Boudry, Laure Saujet, Christophe Pichon, Odile Sismeiro, Ekaterina Semenova, Konstantin Severinov, Chantal Le Bouguenec, Jean-Yves Coppée, Bruno Dupuy, Isabelle Martin-Verstraete (+1 others)
2013 PLoS Genetics  
Expression of each of 16 predicted c-di-GMP-responsive riboswitches was observed, and experimental evidence for their regulatory role in coordinated control of motility and biofilm formation was obtained  ...  This global experimental approach identified 251 putative regulatory sRNAs including 94 potential trans riboregulators located in intergenic regions, 91 cis-antisense RNAs, and 66 riboswitches.  ...  Rosinski-Chupin for invaluable assistance with 59-end RNA-seq design and to I. Poquet for helpful discussions. Author Contributions  ... 
doi:10.1371/journal.pgen.1003493 pmid:23675309 pmcid:PMC3649979 fatcat:wz6yyfwnkrclzmf4vzcqpn5pae

Post-transcriptional gene regulation by an Hfq-independent small RNA in Caulobacter crescentus

Kathrin S Fröhlich, Konrad U Förstner, Zemer Gitai
2018 Nucleic Acids Research  
These findings have implications for the mechanism and evolution of sRNA function across bacterial species.  ...  Bacterial small RNAs (sRNAs) are a heterogeneous group of post-transcriptional regulators that often act at the heart of large networks.  ...  Jacobs-Wagner (Yale University) and U. Jenal (Basel University) for sharing strains, and A. Siryaporn for help with the microarray experiment. We further thank K.  ... 
doi:10.1093/nar/gky765 pmid:30165530 fatcat:f5b4ar3mnzbgphcykowmpujlu4

Sequence-Based Analysis Uncovers an Abundance of Non-Coding RNA in the Total Transcriptome of Mycobacterium tuberculosis

Kristine B. Arnvig, Iñaki Comas, Nicholas R. Thomson, Joanna Houghton, Helena I. Boshoff, Nicholas J. Croucher, Graham Rose, Timothy T. Perkins, Julian Parkhill, Gordon Dougan, Douglas B. Young, William R. Bishai
2011 PLoS Pathogens  
regulatory networks will play an important role in these adaptive responses.  ...  , and intergenic small RNA (sRNA) molecules.  ...  George's, University of London) for the supply of the M. tuberculosis microarrays and advice, and the Wellcome Trust funding of the multicollaborative microbial pathogen microarray facility under its Functional  ... 
doi:10.1371/journal.ppat.1002342 pmid:22072964 pmcid:PMC3207917 fatcat:iqocxibocnbnhbk5u7guvvx3he
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