Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Escherichia coli Lrp regulates one-third of the genome via direct, cooperative, and indirect paths

ABSTRACT: Escherichia coli Lrp regulates one-third of the genome via direct, cooperative, and indirect paths

PROVIDER: PRJNA438455 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Escherichia coli Lrp regulates one-third of the genome via direct, cooperative, and indirect paths

Project description:The global regulator Lrp plays a crucial role in regulating metabolism, virulence and motility in response to environmental conditions. Lrp has previously been shown to activate or repress approximately 10% of genes in Escherichia coli. However, the full spectrum of targets, and how Lrp acts to regulate them, has stymied earlier study. We have combined matched ChIP-seq and RNA sequencing under nine physiological conditions to map the binding and regulatory activity of Lrp as it directs responses to nutrient abundance. In addition to identifying hundreds of novel Lrp targets, we observe two new global trends: first, that Lrp will often bind to promoters in a poised position under conditions when it has no regulatory activity, and second, that nutrient levels induce a global shift in the equilibrium between non-specific and sequence-specific DNA binding. The overall regulatory behavior of Lrp, which as we now show regulates 35% of E. coli genes directly or indirectly under at least one condition, thus arises from the interaction between changes in Lrp binding specificity and cooperative action with other regulators.

2018-11-28 | GSE111874 | GEO

Escherichia coli Lrp Regulates One-Third of the Genome via Direct, Cooperative, and Indirect Routes.

Project description: Not available

| S-EPMC6349092 | biostudies-literature

High throughput analysis of binding of E. coli Lrp mutants

Project description:Feast-Famine Response Proteins are a widely conserved class of global regulators in prokaryotes, the most highly studied of which is the E. coli leucine-responsive regulatory protein (Lrp). Lrp senses environmental nutrition status and subsequently regulates up to one-third of the genes in E. coli, either directly or indirectly. Lrp exists predominantly as octamers and hexadecamers (16mers), where leucine is believed to shift the equilibrium towards the octameric state. In this study, we analyzed the effects of three oligomerization state mutants of Lrp in terms of their ability to bind to DNA and regulate gene expression in response to exogenous leucine. We find that oligomerization beyond dimers is required for Lrp’s regulatory activity, and that contrary to prior speculation, exogenous leucine modulates Lrp activity at its target promoters exclusively by inhibiting Lrp binding to DNA. We also find evidence that Lrp binding bridges DNA over length scales of multiple kilobases, revealing a new range of mechanisms for Lrp-mediated transcriptional regulation.

2023-01-31 | GSE198120 | GEO

Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins

Project description:This SuperSeries is composed of the following subset Series: GSE34992: Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (splice array) GSE34993: Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (CLIP-Seq) GSE34995: Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (RNA-Seq) Refer to individual Series

2012-02-20 | E-GEOD-34996 | biostudies-arrayexpress

Adaptation in protein fitness landscapes is facilitated by indirect paths.

Project description: Not available

| S-EPMC4985287 | biostudies-literature

Multiple paths to cold tolerance

Project description:Multiple paths to cold tolerance: the role of environmental cues, morphological traits and the circadian clock gene vrille

| PRJEB45370 | ENA

Project description:Adaptation in an RNA fitness landscape is constrained by indirect paths

| PRJEB38746 | ENA

Single cell transcriptional profile of third instar larval wing discs in Drosophila

Project description:Our study focuses on understanding the early transcriptional changes taking place during the divergence of the adult muscle precursors that give rise to indirect flight muscles and direct flight muscles in Drosophila. We analyzed the heterogenous cell population of the adult muscle precursors by scRNA-seq and build an integrated single-cell reference atlas. We addressed the differences among muscle-type and different cell state during myoblast differentiation. Also, our dataset includes the transcriptional profile of the epithelial cells localized in the presumptive hinge and notum of third instar larval wing discs. In addition we studied the functional relevance of Amalgam in flight muscle development by depleting Ama expression specifically in the adult muscle precursors. We determined the transcriptional changes and perturbations in AMP cell identity upon Ama knockdown.

2020-08-31 | E-MTAB-9444 | biostudies-arrayexpress

Identification of a new pathway for Th1 cell development induced by cooperative stimulation with IL-4 and TGFbeta

Project description:This SuperSeries is composed of the following subset Series: GSE36520: Identification of a new pathway for Th1 cell development induced by cooperative stimulation with IL-4 and TGFbeta [Affymetrix] GSE36554: Identification of a new pathway for Th1 cell development induced by cooperative stimulation with IL-4 and TGFbeta [Agilent] Refer to individual Series

2012-03-17 | E-GEOD-36556 | biostudies-arrayexpress

Mapping distinct bone marrow niche populations and their differentiation paths

Project description:Mapping distinct bone marrow niche populations and their differentiation paths

| PRJNA546231 | ENA