Regulon

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Regulon

Thank you for visiting nature. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser or turn off compatibility mode in Internet Explorer. In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript. Regulons are the basic units of the response system in a bacterial cell and each consists of a set of transcriptionally co-regulated operons. Regulon elucidation is the basis for studying the bacterial global transcriptional regulation network. In this study, we designed a novel co-regulation score between a pair of operons based on accurate operon identification and cis regulatory motif analyses, which can capture their co-regulation relationship much better than other scores. Taking full advantage of this discovery, we developed a new computational framework and built a novel graph model for regulon prediction. This model integrates the motif comparison and clustering and makes the regulon prediction problem substantially more solvable and accurate. To evaluate our prediction, a regulon coverage score was designed based on the documented regulons and their overlap with our prediction; and a modified Fisher Exact test was implemented to measure how well our predictions match the co-expressed modules derived from E.

Journal of Bacteriology.

In molecular genetics , a regulon is a group of genes that are regulated as a unit, generally controlled by the same regulatory gene that expresses a protein acting as a repressor or activator. This terminology is generally, although not exclusively, used in reference to prokaryotes , whose genomes are often organized into operons ; the genes contained within a regulon are usually organized into more than one operon at disparate locations on the chromosome. A modulon is a set of regulons or operons that are collectively regulated in response to changes in overall conditions or stresses, but may be under the control of different or overlapping regulatory molecules. The term stimulon is sometimes used to refer to the set of genes whose expression responds to specific environmental stimuli. Commonly studied regulons in bacteria are those involved in response to stress such as heat shock.

Thank you for visiting nature. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser or turn off compatibility mode in Internet Explorer. In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript. This protocol explains how to perform a fast SCENIC analysis alongside standard best practices steps on single-cell RNA-sequencing data using software containers and Nextflow pipelines.

Regulon

In molecular genetics , a regulon is a group of genes that are regulated as a unit, generally controlled by the same regulatory gene that expresses a protein acting as a repressor or activator. This terminology is generally, although not exclusively, used in reference to prokaryotes , whose genomes are often organized into operons ; the genes contained within a regulon are usually organized into more than one operon at disparate locations on the chromosome. A modulon is a set of regulons or operons that are collectively regulated in response to changes in overall conditions or stresses, but may be under the control of different or overlapping regulatory molecules. The term stimulon is sometimes used to refer to the set of genes whose expression responds to specific environmental stimuli. Commonly studied regulons in bacteria are those involved in response to stress such as heat shock. The heat shock response in E. Regulons involving virulence factors in pathogenic bacteria are of particular research interest; an often-studied example is the phosphate regulon in E. The Ada regulon in E.

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On the other hand, we defined the regulon coverage score for a known regulon as Ma et al. Hindre T. Nucleic Acids Res 39, e Five regulons containing DEGs and having the corresponding TF at the same time were bolded, being computationally verified as the regulons responsible for acid stress in MG It brings great challenges in algorithm design. Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily. With the new framework, people can identify all encoded regulons for any newly sequenced complete genome systematically, which could be applied to elucidate global transcriptional regulatory network and associated metabolic pathways. However, there are two technical issues: i the constructed graphs are generally quite noisy, leading to high false positive predictions and ii the cliques alone are not adequate to capture the majority of the regulons, hence leading high false negative predictions. All authors submitted comments, read and approved the final manuscript. Systems-level understanding of ethanol-induced stresses and adaptation in E.

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It has been widely applied in dairy fermentations, such as cheese and milk product [ 22 ]. Science , — Quantifying similarity between motifs. Koebmann B. Huang, Y. Nucleic Acids Res 37, D— Dennis D. First of all, we used BOBRO to identify all statistically significant motifs in regulatory promoters P A for each operon A in target genome as described in previous section. And the updated label sets in G will benefit the regulon identification showcased in the next sub-section. Besides, identifying all heavy sub-graphs in a weighted graph itself is NP-hard. Nucleic Acids Res 32, — However, there is no information that can guide the experimental design to have every regulon in a bacterium be activated. In addition, we retrieved 2, operons of the target genome E. Million M. Cite this article Liu, B.