Journal ArticleDOI
Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis
Pierre Nicolas,Ulrike Mäder,Etienne Dervyn,Tatiana Rochat,Aurélie Leduc,Nathalie Pigeonneau,Elena Bidnenko,Elodie Marchadier,Mark Hoebeke,Stéphane Aymerich,Dörte Becher,Paola Bisicchia,Eric Botella,Olivier Delumeau,Geoff Doherty,Emma L. Denham,Mark J. Fogg,Vincent Fromion,Anne Goelzer,Annette Hansen,Elisabeth Härtig,Colin R. Harwood,Georg Homuth,Hanne Østergaard Jarmer,Matthieu Jules,Edda Klipp,Ludovic Le Chat,François Lecointe,Peter J. Lewis,Wolfram Liebermeister,Anika March,Ruben A. T. Mars,Priyanka Nannapaneni,David Noone,Susanne Pohl,Bernd Rinn,Frank Rügheimer,Praveen K. Sappa,Franck Samson,Marc Schaffer,Benno Schwikowski,Leif Steil,Jörg Stülke,Thomas Wiegert,Kevin M. Devine,Anthony J. Wilkinson,Jan Maarten van Dijl,Michael Hecker,Uwe Völker,Philippe Bessières,Philippe Noirot +50 more
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TLDR
The transcriptomes of Bacillus subtilis exposed to a wide range of environmental and nutritional conditions that the organism might encounter in nature are reported, offering an initial understanding of why certain regulatory strategies may be favored during evolution of dynamic control systems.Abstract:
Bacteria adapt to environmental stimuli by adjusting their transcriptomes in a complex manner, the full potential of which has yet to be established for any individual bacterial species. Here, we report the transcriptomes of Bacillus subtilis exposed to a wide range of environmental and nutritional conditions that the organism might encounter in nature. We comprehensively mapped transcription units (TUs) and grouped 2935 promoters into regulons controlled by various RNA polymerase sigma factors, accounting for ~66% of the observed variance in transcriptional activity. This global classification of promoters and detailed description of TUs revealed that a large proportion of the detected antisense RNAs arose from potentially spurious transcription initiation by alternative sigma factors and from imperfect control of transcription termination.read more
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Journal ArticleDOI
Single-cell RNA-seq: advances and future challenges
TL;DR: An overview of the biological questions single-cell RNA-seq has been used to address, the major findings obtained from such studies, and current challenges and expected future developments in this booming field are provided.
Journal ArticleDOI
Gene regulation by antisense transcription
TL;DR: The genomic arrangement of antisense RNAs opposite sense genes indicates that they might be part of self-regulatory circuits that allow genes to regulate their own expression.
Book ChapterDOI
Small RNAs in bacteria and archaea: who they are, what they do, and how they do it
TL;DR: Based on the properties that distinguish sRNA-type from transcription factors-type control, the authors begin to glimpse why sRNAs have evolved as a second, essential layer of gene regulation.
Journal ArticleDOI
Cyclic di-AMP: another second messenger enters the fray
TL;DR: An overview of the synthesis and regulation of cyclic di-AMP (c-di-AMP), one of the latest cyclic nucleotide second messengers to be discovered in bacteria, is provided.
Journal ArticleDOI
Bacillus subtilis: from soil bacterium to super-secreting cell factory.
TL;DR: The engineering of B. subtilis into a next-generation super-secreting cell factory requires combined Systems and Synthetic Biology approaches and can be optimized from the single molecule to the network level while, at the same time, taking into account the balanced use of cellular resources.
References
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Journal ArticleDOI
Improved tools for biological sequence comparison.
TL;DR: Three computer programs for comparisons of protein and DNA sequences can be used to search sequence data bases, evaluate similarity scores, and identify periodic structures based on local sequence similarity.
BookDOI
Markov Chain Monte Carlo in Practice
TL;DR: The Markov Chain Monte Carlo Implementation Results Summary and Discussion MEDICAL MONITORING Introduction Modelling Medical Monitoring Computing Posterior Distributions Forecasting Model Criticism Illustrative Application Discussion MCMC for NONLINEAR HIERARCHICAL MODELS.
Journal ArticleDOI
Reversible jump Markov chain Monte Carlo computation and Bayesian model determination
TL;DR: In this article, the authors propose a new framework for the construction of reversible Markov chain samplers that jump between parameter subspaces of differing dimensionality, which is flexible and entirely constructive.
Journal ArticleDOI
The calculation of posterior distributions by data augmentation
Martin A. Tanner,Wing Hung Wong +1 more
TL;DR: If data augmentation can be used in the calculation of the maximum likelihood estimate, then in the same cases one ought to be able to use it in the computation of the posterior distribution of parameters of interest.
Journal ArticleDOI
Mauve: multiple alignment of conserved genomic sequence with rearrangements.
TL;DR: This work presents methods for identification and alignment of conserved genomic DNA in the presence of rearrangements and horizontal transfer and evaluated the quality of Mauve alignments and drawn comparison to other methods through extensive simulations of genome evolution.
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