Biology subjects

Pineau, M.

Publications and source records attributed to Pineau, M..

3 recordsLinked to original sources

bioRxiv2023

Quantitative spatial analysis of bacterial transcriptome and chromosome structural data with GRATIOSA: application to twin-supercoiled domain distribution

While classical models of transcriptional regulation focus on transcription factors binding at promoters, gene expression is also influenced by chromosome organization. Understanding this spatial regulation strongly benefits from integrated and quantitative spatial analyses of genome-scale data such as RNA-Seq and ChIP-Seq. We introduce Genome Regulation Analysis Tool Incorporating Organization and Spatial Architecture (GRATIOSA), a Python package making such combined analyses more automatic, systematic and reproducible. While current software focuses on initial analysis steps (read mapping and counting), GRAsTIOSA proposes an integrated framework for subsequent analyses, providing a broad range of spatially-resolved quantitative data comparisons and representations. As an example, we quantitatively assess the validity and extension of the twin-supercoiled domain model in Escherichia coli genome-wide transcription, using recent topoisomerase ChIP-Seq data. We show that topoisomerases are locally recruited by the 40% most highly expressed transcription units, with a magnitude correlating with the expression level. The recruitment of topoisomerase I extends to around 10 kb upstream, whereas DNA gyrase is recruited at least 30 kb downstream of transcription units. This organization is the primary determinant of topoisomerase I recruitment, whereas gyrase binding is additionally modulated at larger 100-200 kb length-scale. Further analyses of spatial regulation will be facilitated by GRATIOSA.

bioinformatics↗

bioRxiv2021

What is a supercoiling-sensitive gene? Insights from topoisomerase I inhibition in the Gram-negative bacterium Dickeya dadantii

DNA supercoiling is an essential mechanism of bacterial chromosome compaction, whose level is mainly regulated by topoisomerase I and DNA gyrase. Inhibiting either of these enzymes with antibiotics leads to global supercoiling modifications and subsequent changes in global gene expression. In previous studies, genes responding to DNA relaxation induced by gyrase inhibition were categorised as "supercoiling-sensitive". Here, we studied the opposite variation of DNA supercoiling in the phytopathogen Dickeya dadantii using the non-marketed antibiotic seconeolitsine. We showed that the drug is active against topoisomerase I from this species, and analysed the first transcriptomic response of a Gram-negative bacterium to topoisomerase I inhibition. We find that the responding genes essentially differ from those observed after DNA relaxation, and further depend on the growth phase. We characterised these genes at the functional level, and also detected distinct patterns in terms of expression level, spatial and orientational organisation along the chromosome. Altogether, these results highlight that the supercoiling-sensitivity is a complex feature, which depends on the action of specific topoisomerases, on the physiological conditions, and on their genomic context. Based on previous in vitro expression data of several promoters, we propose a qualitative model of SC-dependent regulation that accounts for many of the contrasting transcriptomic features observed after gyrase or topoisomerase I inhibition.

genomics↗

bioRxiv2020

Bacterial promoter opening underpins ubiquitous transcriptional regulation by DNA supercoiling

DNA supercoiling acts as a global transcriptional regulator, which contributes to the rapid transcriptional response of bacteria to many environmental changes. Although a large fraction of promoters from distant species respond to superhelical variations, the sequence or structural determinants of this behaviour remain elusive. Here, we propose the sequence of the "discriminator" element located downstream of the -10 hexamer to play an important role in this response, by modulating the facility of open-complex formation during transcription initiation. We develop a quantitative model of this regulatory mechanism relying on known parameters of DNA thermodynamics, and show that its predictions quantitatively match the in vitro and in vivo supercoiling response of stable RNA promoters previously measured, as well as the in vivo response of selected mRNA promoters with mutated discriminator sequences. We then test the universality of this mechanism by statistical analysis of promoter sequences in transcriptomes of phylogenetically distant bacteria under conditions of supercoiling variations, (1) by gyrase inhibitors, (2) by environmental stresses, (3) inherited in the longest-running evolution experiment. In all cases, we identify a robust and significant sequence signature in the discriminator region, suggesting that promoter opening underpins an ubiquitous regulatory mechanism in the prokaryotic kingdom, based on the fundamental mechanical properties of DNA.

microbiology↗