Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptional Coupling of Distant Regulatory Genes in Living Embryos

ABSTRACT: The prevailing view of metazoan gene regulation is that individual genes are independently regulated by their own dedicated sets of transcriptional enhancers. Past studies reported long-range gene-gene associations, but their functional significance in regulating transcription remains uncertain and controversial. Here we employ quantitative single cell live imaging methods to provide the first demonstration of co-dependent transcriptional dynamics of genes separated by large genomic distances in living embryos. We find extensive physical and functional associations of distant paralogous genes, including co-regulation by shared enhancers and co-transcriptional bursting over distances of nearly 250kb. Regulatory inter-connectivity depends on promoter-proximal tethering elements and perturbations in these elements uncouple transcription and alter the bursting dynamics of distant genes, suggesting a role of genome topology in the formation and stability of co-transcriptional hubs. Transcriptional coupling of distant genes throughout the Drosophila genome underlies a broad spectrum of conserved developmental processes, suggesting a general strategy for long-range integration of gene activities.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE173518 | GEO | 2022/02/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Chromosome-level organization of the regulatory genome in the Drosophila nervous system [Hi-C]

Project description:Here we present evidence for a new level of genome folding, whereby distant domains megabases apart fuse to form meta-domains. Within meta-domains, certain gene promoters pair with structural intergenic elements in the distant TAD. These long-range associations occur in a large fraction of Drosophila neurons, but support transcription in only a subset of cells in the nervous system. Most of the associated genes encode neuronal determinants, including those engaged in axonal guidance and adhesion. Meta-domains are formed by diverse transcription factors that are able to pair over long and flexible distances. We present evidence that one of these factors, GAF, plays a direct role in this process.

2023-08-01 | GSE214704 | GEO

Chromosome-level organization of the regulatory genome in the Drosophila nervous system

Project description:Past studies have identified topologically associating domains (TADs) as basic units of genome organization. Here, we present evidence for a new level of genome folding, whereby distant TAD pairs megabases apart interact to form meta-domains. Within meta-domains, gene promoters and structural intergenic elements present in distant TADs are specifically paired. The associated genes encode neuronal determinants, including those engaged in axonal guidance and adhesion. These long-range associations occur in a large fraction of neurons but support transcription in only a subset of neurons. Meta-domains are formed by diverse transcription factors that are able to pair over long and flexible distances. We present evidence that two such factors, GAF and CTCF, play direct roles in this process. The relative simplicity of higher-order meta-domain interactions in Drosophila, compared with those previously described in mammals, allowed the demonstration that genomes can fold into highly specialized cell type-specific scaffolds that enable megabase-scale regulatory associations.

2023-08-01 | GSE228095 | GEO

Next Generation Sequencing analysis of Functional Interactions among Insulator Proteins [Beaf-32 ChIP-seq]

Project description:Eukaryotic chromosomes are partitioned into topologically associating domains (TADs) that are demarcated by distinct insulator-binding proteins (IBPs) in Drosophila. Whether IBPs regulate specific long-range contacts and how this may impact gene expression remains unclear. Here we identify ‘indirect peaks’ of multiple IBPs, that represent their distant sites of interactions through long-range contacts. Indirect peaks depend on protein-protein interactions among multiple IBPs and their common co-factors, including CP190, as confirmed by high-resolution analyses of long-range contacts. Mutant IBPs unable to interact with CP190 impair long-range contacts as well as the expression of hundreds of distant genes that are specifically flanked by indirect peaks. Regulation of distant genes strongly correlates with RNAPII pausing, highlighting how this key transcriptional stage may trap insulator-based long-range interactions. Our data illustrate how indirect peaks may decipher gene regulatory networks through specific long-range interactions. Binding profiles of Beaf-32 in Drosophila S2 cells by ChIP-Seq (Illumina)

2014-02-01 | E-GEOD-52962 | biostudies-arrayexpress

Next Generation Sequencing analysis of Functional Interactions among Insulator Proteins [Beaf-32 ChIP-seq]

2014-02-01 | GSE52962 | GEO

Next Generation Sequencing analysis of Functional Interactions among Insulator Proteins [CP190 ChIP-Seq]

2014-02-01 | GSE52886 | GEO

Next Generation Sequencing analysis of Functional Interactions among Insulator Proteins [RNA-Seq]

2014-02-01 | GSE52884 | GEO

Next Generation Sequencing analysis of Functional Interactions among Insulator Proteins [RNA-Seq]

Project description:Eukaryotic chromosomes are partitioned into topologically associating domains (TADs) that are demarcated by distinct insulator-binding proteins (IBPs) in Drosophila. Whether IBPs regulate specific long-range contacts and how this may impact gene expression remains unclear. Here we identify M-bM-^@M-^Xindirect peaksM-bM-^@M-^Y of multiple IBPs, that represent their distant sites of interactions through long-range contacts. Indirect peaks depend on protein-protein interactions among multiple IBPs and their common co-factors, including CP190, as confirmed by high-resolution analyses of long-range contacts. Mutant IBPs unable to interact with CP190 impair long-range contacts as well as the expression of hundreds of distant genes that are specifically flanked by indirect peaks. Regulation of distant genes strongly correlates with RNAPII pausing, highlighting how this key transcriptional stage may trap insulator-based long-range interactions. Our data illustrate how indirect peaks may decipher gene regulatory networks through specific long-range interactions. mRNA profiles of stably transfected Drosophila S2 cell lines expressing Wild-Type or Mutant Beaf by RNASeq (Illumina/TruSeq), in triplicates

2014-02-01 | E-GEOD-52884 | biostudies-arrayexpress

Next Generation Sequencing analysis of Functional Interactions among Insulator Proteins [CP190 ChIP-Seq]

Project description:Eukaryotic chromosomes are partitioned into topologically associating domains (TADs) that are demarcated by distinct insulator-binding proteins (IBPs) in Drosophila. Whether IBPs regulate specific long-range contacts and how this may impact gene expression remains unclear. Here we identify ‘indirect peaks’ of multiple IBPs, that represent their distant sites of interactions through long-range contacts. Indirect peaks depend on protein-protein interactions among multiple IBPs and their common co-factors, including CP190, as confirmed by high-resolution analyses of long-range contacts. Mutant IBPs unable to interact with CP190 impair long-range contacts as well as the expression of hundreds of distant genes that are specifically flanked by indirect peaks. Regulation of distant genes strongly correlates with RNAPII pausing, highlighting how this key transcriptional stage may trap insulator-based long-range interactions. Our data illustrate how indirect peaks may decipher gene regulatory networks through specific long-range interactions. Binding profiles of CP190 in stably transfected Drosophila S2 cell lines expressing in Wild-Type Beaf (Control) or Mutant Beaf by ChIP-Seq (Illumina)

2014-02-01 | E-GEOD-52886 | biostudies-arrayexpress

Transcriptional Bursting and Co-bursting Regulation by Steroid Hormone Release Pattern and Transcription Factor Mobility

Project description:Transcriptional Bursting and Co-bursting Regulation by Steroid Hormone Release Pattern and Transcription Factor Mobility

| PRJNA548190 | ENA

Transcriptional kinetics and molecular functions of long non-coding RNAs

Project description:An increasing number of long non-coding RNAs (lncRNAs) have confirmed important functions, yet little is known about their transcriptional dynamics and it remains challenging to determine their regulatory functions. Here, allele-sensitive single-cell RNA-seq was used to demonstrate that lncRNAs have lower burst frequencies compared to mRNAs. We observed an increased cell-to-cell variability in lncRNA expression that was due to more sporadic bursting (lower frequency) with larger numbers of RNA molecules being produced. Exploiting heterogeneity in asynchronously growing cells, we identified and experimentally validated lncRNAs with cell-state specific functions involved in cell cycle progression and apoptosis. Finally, we identified cis-functioning lncRNAs and knockdown of these lncRNAs modulated either transcriptional burst frequency or size of the nearby protein-coding gene. Collectively, we identify distinct transcriptional regulation of lncRNAs and we demonstrate a role for lncRNAs in the regulation of transcriptional bursting of mRNAs.

2021-11-19 | E-MTAB-11054 | biostudies-arrayexpress

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