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63 results for “supercoiling”
A Genome-Wide Evolutionary Simulation of the Transcription-Supercoiling Coupling: extended version
<p>Data set used for the Artificial Life journal paper <a href="https://direct.mit.edu/artl/article-abstract/28/4/440/112557/A-Genome-Wide-Evolutionary-Simulation-of-the"><em>A Genome-Wide Evolutionary Simulation of the Transcription-Supercoiling Coupling: extended version</em></a>. A preprint of the paper is also available <a href="https://hal.archives-ouvertes.fr/hal-03667822">here</a>.</p> <p>This data is also used in Chapter 4 of my <a href="https://gitlab.inria.fr/tgrohens/phd">PhD thesis</a>.</p>
Supercoiling-mediated feedback simulation dataset
<p><strong>Supercoiling-mediated feedback simulation dataset</strong></p> <p><strong>Background</strong><br> These files represent simulation datasets generated for the publication<br> "Supercoiling-mediated feedback rapidly couples and tunes transcription"<br> by Christopher Johnstone and Kate E. Galloway.</p> <p>All figures in the paper can be replicated by using the code available at <a href="https://github.com/GallowayLabMIT/tangles_model">https://github.com/GallowayLabMIT/tangles_model</a> (<a href="https://doi.org/10.5281/zenodo.7054394">permalink</a>) and these datasets.</p> <p><strong>File summary</strong></p> <ul> <li>`unprocessed_datasets.zip` contains the merged Julia simulation files.</li> <li>`preprocessed_datasets.zip` contains the smaller, preprocessed datasets used for actuall plotting of data figures.</li> </ul> <p><strong>File format</strong></p> <ul> <li>The preprocessed datasets are serialized Pandas dataframes (gzipped Parquet files).</li> <li>The unprocessed datasets are self-describing HDF/H5 files.</li> </ul> <p><strong>Usage</strong><br> The main figure-plotting notebook, `notebooks/modeling_paper_figures.ipynb`, contained in the code repository mentioned above can use either the unprocessed or preprocessed datasets. If the preprocessed datasets are present, it will load them directly. If the preprocessed datasets are not present, that Python notebook will preprocess the data.</p> <p><br> <strong>License</strong><br> This data is available under a CC-BY 4.0 International License.<br> Please attribute:</p> <ul> <li>Christopher Johnstone (cjohnsto@mit.edu)</li> <li>Kate E. Galloway (katiegal@mit.edu)</li> </ul>
Dissecting the in vivo dynamics of transcription locking due to positive supercoiling buildup
<p>Positive supercoiling buildup (PSB) is a pervasive phenomenon in the transcriptional programs of Escherichia coli. After finding a range of Gyrase concentrations where the inverse of the transcription rate of a chromosome-integrated gene changes linearly with the inverse of Gyrase concentration, we apply a Line Weaver-Burk plot to dissect the expected in vivo transcription rate in absence of PSB. We validate the estimation by time-lapse microscopy of single-RNA production kinetics of the same gene when single-copy plasmid-borne, shown to be impervious to Gyrase inhibition. Next, we estimate the fraction of time in locked states and number of transcription events prior to locking, which we validate by measurements under Gyrase inhibition. Replacing the gene of interest by one with slower transcription rate decreases the fraction of time in locked states due to PSB. Finally, we combine data from both constructs to infer a range of possible transcription initiation locking kinetics in a chromosomal location, obtainable by tuning the transcription rate. We validate with measurements of transcription activity at different induction levels. This strategy for dissecting transcription initiation locking kinetics due to PSB can contribute to resolve the transcriptional programs of E. coli and in the engineering of synthetic genetic circuits.</p>
Apical Localization of RNA Polymerases Modulate Transcription Dynamics and Supercoiling Domains Revealed by Cryo-ET
<p>Supplementary materials include all particle raw tilts, 3D reconstructions, models, FSC evaluations, statistical data analyses, gel images, and oxDNA molecular dynamics simulations for the manuscript titled "<strong>Apical Localization of RNA Polymerases Modulate Transcription Dynamics and Supercoiling Domains Revealed by Cryo-ET</strong>".</p>
Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes of E. coli
<p><span>Cold shock adaptability is a key survival skill of gut </span><span>bacteria of warm-blooded animals. <em>Escherichia coli</em> cold shock responses are controlled by a complex multi-gene, timely-ordered transcriptional program. We investigated its underlying mechanisms. Having identified short-term, cold shock repressed genes, we show that their responsiveness is unrelated to their transcription factors or global regulators, while</span><span> their single-cell protein numbers' variability increases after cold shock. We hypothesized that some </span><span>cold shock repressed </span><span>genes could be triggered by high propensity for transcription locking due to changes in DNA supercoiling (likely due to DNA relaxation caused by an overall reduction in negative supercoiling). </span><span>Concomitantly, we found that nearly half of cold shock repressed genes are also highly responsive to gyrase inhibition (albeit most genes responsive to gyrase inhibition are not cold shock responsive). Further, their response strengths to cold shock and gyrase inhibition correlate. Meanwhile, under cold shock, nucleoid density increases, and gyrases and nucleoid become more colocalized. Moreover, the cellular energy decreases, which may hinder positive supercoils resolution. Overall, we conclude that sensitivity to diminished negative supercoiling is a core feature of <em>E. coli</em>'s short-term, cold shock transcriptional program, and could be used to regulate the temperature sensitivity of synthetic circuits.</span></p>
Emergence of Supercoiling-Mediated Regulatory Networks through the Evolution of Bacterial Chromosome Organization
<p>Data generated using <a href="https://gitlab.inria.fr/tgrohens/evotsc">EvoTSC</a> and used in the <a href="https://doi.org/10.24072/pci.mcb.100198">Emergence of Supercoiling-Mediated Regulatory Networks through the Evolution of Bacterial Chromosome Organization</a> paper.</p> <p>This data is also used in Chapter 5 of my <a href="https://gitlab.inria.fr/tgrohens/phd">PhD thesis</a>.</p>
Dissecting the in vivo dynamics of transcription locking due to positive supercoiling buildup
Open the record for dataset details and reuse information.
Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes of E. coli
Open the record for dataset details and reuse information.
ParBF DNA binding profiles over various supercoiling level and on linear DNA
GEO Series GSE256357. Salmonella enterica subsp. enterica serovar Typhimurium str. LT2; Escherichia coli. 18 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Type II topoisomerases shape multi-scale 3D chromatin folding in regions of positive supercoils (LaminB1 CnR).
GEO Series GSE255734. Homo sapiens. 6 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
High-resolution, genome-wide mapping of positive supercoiling in chromosomes [RNA-Seq 2]
GEO Series GSE164186. Saccharomyces cerevisiae. 7 samples. Type: Expression profiling by high throughput sequencing.
Transcription forms and remodels supercoiling domains unfolding large scale chromatin structures [Illumina transcription]
GEO Series GSE43449. Homo sapiens. 3 samples. Type: Expression profiling by array.
Type II topoisomerases shape multi-scale 3D chromatin folding in regions of positive supercoils (Ttchem-seq).
GEO Series GSE255737. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing; Other.
Saccharomyces cerevisiae cells: control vs positive supercoiling accumulation after 0, 30 and 120 min
GEO Series GSE18240. Saccharomyces cerevisiae. 9 samples. Type: Expression profiling by array.
Saccharomyces cerevisiae cells: control vs positive supercoiling accumulation
GEO Series GSE18242. Saccharomyces cerevisiae. 21 samples. Type: Expression profiling by array.
An increase in negative supercoiling in bacteria reveals topology-reacting gene clusters and a homeostatic response mediated by the DNA topoisomerase I gene [array]
GEO Series GSE77587. Streptococcus pneumoniae R6. 8 samples. Type: Expression profiling by array.
Transcription dependent dynamic supercoiling in Raji human B cells in vivo
GEO Series GSE43751. Homo sapiens. 12 samples. Type: Genome variation profiling by genome tiling array.
High-resolution, genome-wide mapping of positive supercoiling in chromosomes
GEO Series GSE152882. Escherichia coli str. K-12 substr. MG1655; Saccharomyces cerevisiae. 28 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes of E. coli
GEO Series GSE194037. Escherichia coli str. K-12 substr. MG1655. 15 samples. Type: Expression profiling by high throughput sequencing.
Control of RNA polymerase II promoter-proximal pausing by DNA supercoiling [RNA-seq]
GEO Series GSE141799. Homo sapiens. 10 samples. Type: Expression profiling by high throughput sequencing.
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International Brain Laboratory public data
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OpenNeuro
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