Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Toll-Like Receptor-Induced Nucleosome Remodeling Achieved by Broadly Acting NF-kB in Collaboration with Transcription Factors Conferring Selectivity [RNA-Seq]

ABSTRACT: Macrophages play a critical role in bridging the innate and adaptive immune systems, which requires timely and precise transcription control when responding to danger signals. Gene expression networks in macrophages have been profiled extensively in recent decades with the advancement of high-throughput sequencing technologies. However, unveiling critical mechanistic insights into control of diverse transcriptional networks has proven to be challenging. Recent evidence has suggested that the accessibility of chromatin structure can provide an integral means of transcription regulation. We have used the relatively recent Assay for Transposase-Accessible Chromatin using Sequencing (ATAC-seq) method to assess chromatin accessibility with optimal resolution in mouse bone marrow derived macrophages during the course of lipid- A stimulation. This advanced method enabled us to characterize the chromatin state of genome-wide regulatory regions. By applying a quantitative systematic approach, we obtained mechanistic insights into the highly selective role of the major transcription factors, NF-κB and IRF3, in nucleosome remodeling and transcription regulation.

ORGANISM(S): Mus musculus

PROVIDER: GSE235282 | GEO | 2024/01/16

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Toll-Like Receptor-Induced Nucleosome Remodeling Achieved by Broadly Acting NF-kB in Collaboration with Transcription Factors Conferring Selectivity [BMDM_ATAC_2]

Project description:Macrophages play a critical role in bridging the innate and adaptive immune systems, which requires timely and precise transcription control when responding to danger signals. Gene expression networks in macrophages have been profiled extensively in recent decades with the advancement of high-throughput sequencing technologies. However, unveiling critical mechanistic insights into control of diverse transcriptional networks has proven to be challenging. Recent evidence has suggested that the accessibility of chromatin structure can provide an integral means of transcription regulation. We have used the relatively recent Assay for Transposase-Accessible Chromatin using Sequencing (ATAC-seq) method to assess chromatin accessibility with optimal resolution in mouse bone marrow derived macrophages during the course of lipid- A stimulation. This advanced method enabled us to characterize the chromatin state of genome-wide regulatory regions. By applying a quantitative systematic approach, we obtained mechanistic insights into the highly selective role of the major transcription factors, NF-κB and IRF3, in nucleosome remodeling and transcription regulation.

2024-01-16 | GSE248432 | GEO

Toll-Like Receptor-Induced Nucleosome Remodeling Achieved by Broadly Acting NF-kB in Collaboration with Transcription Factors Conferring Selectivity [ATAC_MQ]

2024-01-16 | GSE234913 | GEO

Toll-Like Receptor-induced Nucleosome Remodeling Achieved by Broadly Acting NF-kB in Collaboration with Transcription Factors Conferring Selectivity [BMDM_ATAC]

2024-01-12 | GSE234694 | GEO

Toll-Like Receptor-Induced Nucleosome Remodeling Achieved by Broadly Acting NF-kB in Collaboration with Transcription Factors Conferring Selectivity [ChIP-Seq]

2024-01-16 | GSE235281 | GEO

The transcription factor NF-κB orchestrates nucleosome remodeling during the primary response to Toll-like receptor 4 signaling [CHiC]

2024-06-21 | GSE270366 | GEO

The transcription factor NF-κB orchestrates nucleosome remodeling during the primary response to Toll-like receptor 4 signaling [4C]

2024-06-21 | GSE270365 | GEO

A Stringent Systems Approach Uncovers Gene-Specific Mechanisms Regulating Inflammation [ATAC-seq]

Project description:Much has been learned about transcriptional cascades and networks from large-scale systems analyses of high-throughput data sets. However, analysis methods that optimize statistical power through simultaneous evaluation of thousands of ChIP-seq peaks or differentially expressed genes possess substantial limitations in their ability to uncover mechanistic principles of transcriptional control. By examining nascent transcript RNA-seq, ChIP-seq, and binding motif data sets from lipid A-stimulated macrophages with increased attention to the quantitative distribution of signals, we identified unexpected relationships between the in vivo binding properties of inducible transcription factors, motif strength, and transcription. Furthermore, rather than emphasizing common features of large clusters of co-regulated genes, our results highlight the extent to which unique mechanisms regulate individual genes with key biological functions. Our findings demonstrate the mechanistic value of stringent interrogation of well-defined sets of genes as a complement to broader systems analyses of transcriptional cascades and networks. Bone marrow-derived macrophages were stimulated with lipid A for 0 or 120 minutes. Chromatin was treated with Tn5 transposase to measure DNA accessibility

2016-01-18 | E-GEOD-74191 | biostudies-arrayexpress

Evolution of diapause in the African killifish by remodeling ancient gene regulatory landscape

Project description:Suspended animation (e.g. hibernation, diapause) allows organisms to survive extreme environments. But the mechanisms underlying the evolution of suspended animation states are unknown. The African turquoise killifish has evolved diapause as a form of suspended development to survive the complete drought that occurs every summer. Here, we show that gene duplicates – paralogs – exhibit specialized expression in diapause compared to normal development in the African turquoise killifish. Surprisingly, paralogs with specialized expression in diapause are evolutionarily very ancient and are present even in vertebrates that do not exhibit diapause. To determine if evolution of diapause is due to the regulatory landscape rewiring at ancient paralogs, we assessed chromatin accessibility genome-wide in fish species with or without diapause. This analysis revealed an evolutionary recent increase in chromatin accessibility at very ancient paralogs in African turquoise killifish. The increase in chromatin accessibility is linked to the presence of new binding sites for transcription factors, likely due to de novo mutations and transposable element (TE) insertion. Interestingly, accessible chromatin regions in diapause are enriched for lipid metabolism genes, and our lipidomics studies uncover a striking difference in lipid species in African turquoise killifish diapause, which could be critical for long-term survival. Together, our results show that diapause likely originated by repurposing pre-existing gene programs via recent changes in the regulatory landscape. This work raises the possibility that suspended animation programs could be reactivated in other species for long-term preservation via transcription factor remodeling and suggests a mechanism for how complex adaptations evolve in nature.

2021-08-05 | ST001898 | MetabolomicsWorkbench

FOXA2 controls the anti-oxidant response in FH-deficient cells independent of NRF2

Project description:Hereditary Leiomyomatosis and renal cell cancer is caused by fumarate hydratase loss of heterozygosity and subsequence accumulation of fumarate. Fumarate is known to activate the anti-oxidant response and is key for cellular survival. Fumarate succinates KEAP1 which releases NRF2 to activate the antioxidant response. The role of fumarate on the global regulatory chromatin landscape is less understood. Here, by integrating chromatin accessibility and histone ChIP-seq profiles, we identify complex transcription factor networks involved in the highly remodelled chromatin landscape of FH-deficient cells. We implicate FOXA2 in the maintenance of FH-deficient cells by regulating anti-oxidant response genes and subsequent metabolic output, independent of NRF2. These results identify new redox and amino acid metabolism regulators and provide new avenues for therapeutic intervention.

2022-06-01 | ST002199 | MetabolomicsWorkbench

Dual DNA/protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia

Project description:The architecture of chromatin specifies eukaryotic cell identity by controlling transcription factor access to sites of gene regulation. Here we describe a dual transposase/peroxidase approach, integrative DNA And Protein Tagging (iDAPT), which detects both DNA (iDAPT-seq) and protein (iDAPT-MS) associated with accessible regions of chromatin. In addition to direct identification of bound transcription factors, iDAPT enables the inference of their gene regulatory networks, protein interactors, and regulation of chromatin accessibility. We applied iDAPT to profile the epigenomic consequences of granulocytic differentiation of acute promyelocytic leukemia, yielding previously undescribed mechanistic insights with potential therapeutic implications. Our findings demonstrate the power of iDAPT as a discovery platform for both the dynamic epigenomic landscapes and their transcription factor components associated with biological phenomena and disease.

2020-11-02 | PXD022252 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

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