Name: Global analysis of photosynthesis transcriptional regulatory networks [ChIP-seq]
Keywords: ChIP-seq

Omics DI

Browse
Submit Data
Databases
API
Help
Login

Dataset Information

10 Views

35 Connections

0 Citations

0 Reanalyses

3 Downloads

Omics score: 297

Global analysis of photosynthesis transcriptional regulatory networks [ChIP-seq]

ABSTRACT: To gain a deeper understanding of the transcription factors that regulate photosynthesis in Rhodobacter sphaeroides ChIP-seq was used to determine the genome-wide binding locations of 4 transcription factors (FnrL, PrrA, CrpK and RSP_2888) known or predicted to be involved in the regulation of photosynthesis. Genome-wide protein-DNA interaction analysis of 4 transcription factors known or predicted to be involved in the regulation of photosynthesis in Rhodobacter sphaeroides, using ChIP-seq and complementary assays.

ORGANISM(S): Rhodobacter sphaeroides

SUBMITTER: Saheed Imam Timothy J Donohue

PROVIDER: E-GEOD-58716 | ArrayExpress | 2014-12-15

SECONDARY ACCESSION(S): SRP043505GSE58716PRJNA253309

REPOSITORIES: GEO, ArrayExpress, ENA

ACCESS DATA

Json Xml

Publications

Global analysis of photosynthesis transcriptional regulatory networks.

Imam Saheed S Noguera Daniel R DR Donohue Timothy J TJ

PLoS genetics 20141211 12

Photosynthesis is a crucial biological process that depends on the interplay of many components. This work analyzed the gene targets for 4 transcription factors: FnrL, PrrA, CrpK and MppG (RSP_2888), which are known or predicted to control photosynthesis in Rhodobacter sphaeroides. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) identified 52 operons under direct control of FnrL, illustrating its regulatory role in photosynthesis, iron homeostasis, nitrogen metabo ...[more]

PMID: 25503406

Similar Datasets

An Integrated Approach to Reconstructing Genome-scale Transcriptional Regulatory Networks [ChIP-Seq]

Project description:By integrating sequence information from closely related bacteria with a compendium of high-throughput gene expression datasets, a large-scale transcriptional regulatory networks was constructed for Rhodobacter sphaeroides. Predictions from this network were validated in part using genome-wide analysis for 3 transcription factors (PpsR, RSP_0489 and RSP_3341). Genome-wide protein-DNA interaction analysis of 3 transcription factors predicted to be involved in photosynthesis (PpsR), carbon metabolism (RSP_0489) and iron homeostasis (RSP_3341) were used to validate predictions from a large-scale reconstruction of R. sphaeroides transcriptional regulatory network.

2014-07-01 | E-GEOD-58648 | ArrayExpress

Genome-wide protein-DNA interaction analysis of CceR and AkgR transcription factors

Project description:To gain a better understanding of the transcription factors that regulate central carbon metabolism in Rhodobacter sphaeroides ChIP-seq was used to determine the genome-wide binding locations of 2 transcription factors: CceR (RSP_1663) and AkgR (RSP_0981) both predicted to be involved in the regulation of of central carbon and energy metabolism. Genome-wide protein-DNA interaction analysis of 2 transcription factors predicted to be involved in regulation of central carbon metabolism CceR and AkgR

2015-02-02 | E-GEOD-63449 | ArrayExpress

Gene expression profiling and genome-wide maps in PDGFB-induced glioma

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-05-17 | E-GEOD-80089 | ArrayExpress

Genome-wide maps in PDGFB-induced glioma

Project description:We performed genome-wide profiling of oligodendrocyte lineage transcription factor 2 (Olig2) and other histone markers in platelet-derived growth factor subunit B (PDGFB)-induced glioma and genome-occupancy analyses coupled with transcriptome profiling to reveal gene regulatory network. Examination of Olig2, H327Ac, and H3K4me3 genome-wide occupancy in PDGFB-induced Ctrl-T and Olig2cKO brain tumors (gliomas).

2016-05-17 | E-GEOD-80088 | ArrayExpress

Genome-wide maps of chromatin state in HSC, Pro B and mature B cells

Project description:We have used a genome-wide ChIP-sequencing approach to define and investigate the dynamics of the cis-regulatory landscape in three developmental stages of the murine hematopoietic system. To this end, we have compared the profiles of H3K4me3, H3K4me1, H3K27ac, H3K27me3 and H3K9me2 in HSCs, committed pro-B and splenic mature B cells. We find the enhancer repertoire to be dynamically reshaped during hematopoiesis progression, surprisingly only a small fraction of primed enhancers in HSCs or committed progenitors become activated in subsequent stages. In turn, the majority of active enhancers in terminally differentiated cells are not primed in earlier stages. We also found that The heterochromatin mark H3K9me2 covers large domains that remain largerly invariant across the three stages and are depleted in both active chromatin marks and the Polycomb related mark H3K27me3. Investigating enhancer dynamics in 3 different stages of B cell development

2015-10-19 | E-GEOD-60005 | ArrayExpress

Chromatin Remodeler CHD7 mutated in CHARGE Syndrome Interacts with Sox10 to Regulate Timing of CNS Myelination and Remyelination [ChIP-seq]

Project description:Mutations in CHD7, encoding ATP-dependent chromodomain-helicase-DNA-binding protein 7, in CHARGE syndrome leads to multiple congenital anomalies including growth retardation, craniofacial malformations and neurological dysfunction. Currently, mechanisms underlying the CNS phenotypes remain poorly understood. Here, we show that Chd7 is a direct transcriptional target of oligodendrogenesis-promoting factors Olig2 and Brg1 and required for proper timing of CNS myelination and remyelination. Genome-occupancy analyses coupled with transcriptome profiling reveal that Chd7 cooperates with Sox10 to target the enhancers of key myelinogenic genes, and identify novel Chd7 target. Examination of Chd7 and Sox10 genomewide occupancy in differentiating oligodendrocytes

2016-02-29 | E-GEOD-72725 | ArrayExpress

HP1a recruitment to promoters is independent of H3K9 methylation in Drosophila melanogaster

Project description:Heterochromatin protein 1 (HP1) proteins are important regulators of heterochromatin mediated gene silencing and chromosome structure and it is well known as the reader of the heterochromatin mark methylation of histone H3 lysine 9 (H3K9me). In Drosophila three different histone lysine methyl transferases (HKMTs) are associated with the methylation of H3K9; Su(var)3-9, Setdb1 and G9a. To gain insights on the dependence of HP1a on the three different HKMTs, the division of labor between these methyl transferases and the dependence of HP1a on H3K9me we have studied HP1a binding in relation to H3K9me in mutants of these HKMTs. We show that Su(var)3-9 is responsible for the HP1a H3K9me-dependent binding in pericentromeric regions while Setdb1 controls the HP1a H3K9me-dependent binding to cytological region 2L:31 and together with POF chromosome 4. HP1a binds to the promoters and within gene bodies of active genes in these three regions. More importantly, HP1a bound at promoters of active genes are independent of H3K9me and POF and is associated to heterochromatin protein 2 (HP2) and open chromatin. Our results supports a model where HP1a nucleates with high affinity independent of H3K9me in promoters of active genes and then spreads via H3K9 methylation and transient looping contacts with those H3K9me target sites. In total 44 samples; 2 replicates for each genotype and for each ChIP (HP1a, H3K9me2 and H3K9me3)

2012-12-21 | E-GEOD-38366 | ArrayExpress

Targeting of Painting of fourth to roX1 and roX2 proximal sites suggests evolutionary links between dosage compensation and the regulation of the 4th chromosome in Drosophila melanogaster

Project description:In Drosophila melanogaster, two chromosome-specific targeting and regulatory systems have been described. The male-specific lethal (MSL) complex supports dosage compensation by stimulating gene expression from the male X-chromosome and the protein Painting of fourth (POF) specifically targets and stimulates expression from the heterochromatic 4th chromosome. The targeting sites of both systems are well characterized, but the principles underlying the targeting mechanisms have remained elusive. Here we present an original observation, namely that POF specifically targets two loci on the X-chromosome, PoX1 and PoX2 (POF-on-X). PoX1 and PoX2 are located close to the roX1 and roX2 genes, which encode ncRNAs important for the correct targeting and spreading of the MSL-complex. We also found that the targeting of POF to PoX1 and PoX2 is largely dependent on roX expression and identified a high-affinity target region which ectopically recruits POF. The results presented support a model linking the MSL-complex to POF and dosage compensation to regulation of heterochromatin. POF salivary glands ChIP

2013-05-27 | E-GEOD-45402 | ArrayExpress

ChIP-sequencing analysis of RNA Pol II binding sites 4 hours after Myc activation in liver and heart tissue, from wild type and R26CAG-c-MycERT2 mice

Project description:Aim: To determine RNA Pol II binding sites in mouse heart and liver, 4 hours post MycER activation. Pol II ChIP sequencing performed on chromatin isolated from hearts and livers harvested from wild-type (R26+/+) and R26CAG-c-MycERT2/+ mice 4 hours post administration of (Z)-4-hydroxytamoxifen.

2020-03-06 | E-MTAB-7593 | ArrayExpress

ChIP-sequencing analysis of Myc binding sites 4 hours after Myc activation in liver and heart tissue, from wild type and R26CAG-c-MycERT2 mice

Project description:Aim: To determine Myc binding sites in mouse heart and liver, 4 hours post MycER activation. c-Myc ChIP sequencing performed on chromatin isolated from hearts and livers harvested from wild-type (R26+/+) and R26CAG-c-MycERT2/+ mice 4 hours post administration of (Z)-4-hydroxytamoxifen.

2020-02-24 | E-MTAB-7592 | ArrayExpress

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
GPMDB
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub Seek

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data