Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Capture of Associated Targets on Chromatin (CATCH) Links Long-Distance Chromatin Looping to Transcriptional Coordination

ABSTRACT: We describe here a sensitive and novel method of identifying endogenous DNA-DNA interactions. Capture of Associated Targets on CHromatin (CATCH) uses efficient capture and enrichment of specific genomic loci of interest through hybridization and subsequent purification via complementary biotinylated oligonucleotide. The CATCH assay requires no enzymatic digestion or ligation, requires little starting material, provides high quality data, has excellent reproducibility and is completed in less than 24 hours. Efficacy is demonstrated through capture of three disparate loci, which demonstrate unique subsets of long-distance chromatin interactions enriched for both enhancer marks and estrogen receptor binding sites. In each experiment, CATCH-seq peaks representing long-distance chromatin interactions were centered near the TSS of genes, and critically, the genes identified as physically interacting are shown to be transcriptionally co-expressed. These interactions could potentially create transcriptional hubs for the regulation of gene expression programs.

ORGANISM(S): Homo sapiens

PROVIDER: GSE85762 | GEO | 2016/09/22

SECONDARY ACCESSION(S): PRJNA339287

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

4C-seq characterization of Drosophila BEAF binding regions provides evidence for highly variable long-distance interactions between active chromatin

Project description:Chromatin organization is crucial for nuclear functions such as gene regulation, DNA replication and DNA repair. Insulator binding proteins, such as the Drosophila Boundary Element-Associated Factor (BEAF), are involved in chromatin organization. To further understand the role of BEAF, we detected cis- and trans-interaction partners of four BEAF binding regions (viewpoints) using 4C (circular chromosome conformation capture) and analyzed their association with different genomic features. Previous genome-wide mapping found that BEAF usually binds near transcription start sites, often of housekeeping genes, so our viewpoints were selected to reflect this. Our 4C data show the interaction partners of our viewpoints are highly variable and generally enriched for active chromatin marks. The most consistent association was with housekeeping genes, a feature in common with our viewpoints. Fluorescence in situ hybridization indicated that the long-distance interactions occur even in the absence of BEAF. These data are most consistent with a model in which BEAF is redundant with other factors found at active promoters. Our results point to principles of long-distance interactions made by active chromatin, supporting a previously proposed model in which condensed chromatin is sticky and associates into topologically associating domains (TADs) separated by active chromatin. We propose that the highly variable long-distance interactions we detect are driven by redundant factors that open chromatin to promote transcription, combined with active chromatin filling spaces between TADs while packing of TADs relative to each other varies from cell to cell.

2018-08-02 | GSE118013 | GEO

CATCH-IT method for measuring nucleosome turnover

Project description:Direct measurement of nucleosome turnover dynamics by using co-translational incorporation of the methionine (Met) surrogate azidohomoalaine (Aha) into proteins and subsequent ligation of biotin to Aha-containing proteins through the [3+2] cycloaddition reaction between the azide group of Aha and an alkyne linked to biotin. To measure turnover rates, we treat cells briefly with Aha, couple biotin to nucleosomes containing newly incorporated histones, affinity purify with strepavidin, wash stringently to remove non-histone proteins and H2A/H2B dimers, and analyze the affinity-purified DNA using tiling microarrays. We call this strategy 'CATCH-IT' for Covalent Attachment of Tags to Capture Histones and Identify Turnover. Keywords: Chromatin affinity-purification on microarray All experiments were done using strepavidin pulldown DNA cohybridized with total input DNA to the same array. Two channels per array, Cy5 and Cy3, were used in each experiment.

2010-05-27 | E-GEOD-19788 | biostudies-arrayexpress

CATCH-IT method for measuring nucleosome turnover

2010-05-27 | GSE19788 | GEO

Umbilical cord miRNA profile associated with catch-up growth in SGA infants

Project description:The aim of this study was to identify umbilical cord microRNA (miRNA) associated with catch-up growth in SGA infants. miRCURY LNA™ Universal RT microRNA PCR Human Panel I+II (Exiqon) were used to study the miRNA profile in umbilical cord tissue of 5 SGA infants with catch-up (SGA-CU), 5 SGA infants without catch-up (SGA-nonCU) and 5 control infants (appropriate-for-gestational-age, AGA). Catch-up differentially expressed miRNA were studied and validated in a larger cohort.

2019-03-22 | GSE128694 | GEO

Homo sapiens

Project description:Capture of Associated Targets on Chromatin (CATCH) Links Long-Distance Chromatin Looping to Transcriptional Coordination

| PRJNA339287 | ENA

Distance Effect

Project description:Here we show that regions of the honeybee brain involved in visual processing and learning and memory show a genomic response to distance information. Using a method that separates effects of perceived distance from effects of actual distance flown, we found that individuals forced to shift from a short to a perceived long distance to reach a feeding site showed differences in gene expression in the optic lobes and mushroom bodies relative to individuals that continued to perceive flying a short distance.

2011-03-05 | E-TABM-910 | biostudies-arrayexpress

Bovine feedlot catch-basin metagenome

Project description:Bovine feedlot catch-basin metagenome Metagenome

| PRJNA529711 | ENA

Increased long-distance interactions related to heterotic expression in Arabidopsis hybrids

Project description:In plants, the genomic structure of hybrids changed compared with their parents. However, the effects of genomic structure changes on heterotic expression in hybrids remain elusive. By comparing interspecific hybrids between Col×C24 and their backcross C24×Col in Arabidopsis with Hi-C analysis, we found that the three-dimensional (3D) chromatin organization had more long-distance interactions relative to parents. The compartment strength related to the increased A-B compartment interactions decreased in hybrids. In the boundaries of topologically associated domains (TADs) like regions in hybrids, the values of Interchromosomal Fraction of Interactions (ICF) and Distal-to-Local [log2] (DLR) were higher than or close to the highest value of their parents. While in the hybrids of CURLY LEAF (clf) mutants, which affects the long-distance interactions, the heterosis phenotype disappeared and the ICF and DLR in hybrids were lower than their parents. In addition, compared with the clf mutant, the differential expressed genes located in TAD boundaries and loop regions in the wild type changed more obviously. In the long-distance interaction and the loop region between WT and clf, there were obvious differences in the functional enrichment for DEGs. The genes with cell cycle and mitotic related process were specifically enriched in clf. By analyzing ChIP-seq data, we found that the enrichment of H3K27me3 were higher in the hybrids in WT, which may lead to more long-distance interactions. Our findings may therefore propose a new epigenetic explanation of the heterotic expression in Arabidopsis hybrids and provide new insights into crop breeding and yield increasing.

2024-03-24 | GSE221446 | GEO

Increased long-distance interactions related to heterotic expression in Arabidopsis hybrids (clf)

2024-03-24 | GSE222132 | GEO

Chromatin interaction profiles at bivalent genes by multiplexed splinkerette 4C sequencing

Project description:To examine chromatin interaction profiles around bivalent gene loci, we developed a multiplexed splinkerette Chromosome Conformation Capture Combined with high-throughput sequencing (ms4C-seq). By using ms4C-seq, we showed that bivalent gene loci tend to be colocalized in hiPSCs and that the colocalization requires PRC1, PRC2 and TrxG complexes that are the essential regulatory factors for maintenance of developmental genes in the transcriptionally poised state.

2017-11-04 | GSE90782 | GEO

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