Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Tri-4C: efficient and quantitative analysis of enhancer loops at hundred base pair resolution (Tri-4C)

ABSTRACT: Tri-4C: efficient and quantitative analysis of enhancer loops at hundred base pair resolution (Tri-4C)

PROVIDER: PRJNA488421 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Tri-4C: efficient and quantitative analysis of enhancer loops at hundred base pair resolution (Tri-4C)

Project description:Enhancer looping governs gene regulatory circuitry but is challenging to detect. Here we present Tri-4C, an ultrafine mapping method for distal chromatin contacts using triple restriction enzyme (RE) digestion. Tri-4C identifies enhancer loops that are undetectable by current single RE- based methods and reveals quantitative loop strengths in enhancer interaction networks underlying dynamic gene control. This multi-RE approach may be applied to general 3C-derived methods for accurate detection of enhancer loops.

2020-08-28 | GSE119187 | GEO

Tri-4C: efficient and quantitative analysis of enhancer loops at hundred base pair resolution (ATAC-Seq)

2020-08-28 | GSE119188 | GEO

Tri-4C: efficient and quantitative analysis of enhancer loops at hundred base pair resolution

Project description:Tri-4C: efficient and quantitative analysis of enhancer loops at hundred base pair resolution

| PRJNA488419 | ENA

Tri-4C: efficient and quantitative analysis of enhancer loops at hundred base pair resolution (ATAC-Seq)

Project description:Tri-4C: efficient and quantitative analysis of enhancer loops at hundred base pair resolution (ATAC-Seq)

| PRJNA488422 | ENA

Tri-4C: efficient and quantitative analysis of enhancer loops at hundred base pair resolution

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-08-28 | GSE119189 | GEO

Ultrafine Mapping of Chromosome Conformation at hundred basepair resolution reveals regulatory genome architecture

Project description:The resolution limit of chromatin conformation capture methodologies (3Cs) has restrained their application in detection of fine-level chromatin structure mediated by cis-regulatory elements (CREs). Here we report two 3C-derived methods, Tri-4C and Tri-HiC, utilizing mult-restriction enzyme digestions capable of achieveing ultrafine genome digestion for targeted and global chromatin interaction mapping, respectively, at a one hundred basepair resolution. Tri-4C identified loops associated with CREs including those involving regulatory elements devoid of typical epigenomic marks, quantifatively revealing alterations in interaction networks underlying dynamic gene control. Tri-HiC successfully uncovers fine-gage enhancer:promoter (E:P) loops at genome-wide level, identifying > 20-fold more CRE loops than in situ HiC. In addition to refined loop detection, Tri-HiC also reveals interaction stripes and contact domain insulation from promoters and enhancers, revealing their loop extrusion behaviors resembling the topologically-associated domain (TAD) boundaries. Tri-4C and Tri-HiC provide robust approaches to achieve the high resolution interactome maps required for characterizing fine-gage regulatory chromatin interactions in analysis of development, homeostasis and disease.

2021-11-02 | GSE161014 | GEO

CTCF binding polarity determines chromatin looping [4C]

Project description:CCCTC-binding factor (CTCF) is an architectural protein involved in the three-dimensional organization of chromatin. In this study, we systematically assayed the 3D genomic contact profiles of hundreds of CTCF binding sites in multiple tissues with high-resolution 4C-seq. We find both developmentally stable and dynamic chromatin loops. As recently reported, our data also suggest that chromatin loops preferentially form between CTCF binding sites oriented in a convergent manner. To directly test this, we used CRISPR-Cas9 genome editing to delete core CTCF binding sites in three loci, including the CTCF site in the Sox2 super-enhancer. In all instances, CTCF and cohesin recruitment were lost, and chromatin loops with distal CTCF sites were disrupted or destabilized. Re-insertion of oppositely oriented CTCF recognition sequences restored CTCF and cohesin recruitment, but did not re-establish chromatin loops. We conclude that CTCF binding polarity plays a functional role in the formation of higher order chromatin structure. 4C-seq was performed on a large number of viewpoints in E14 embryonic stem cells, neural precursor cells and primary fetal liver cells

2015-10-29 | E-GEOD-72539 | biostudies-arrayexpress

peakC: a flexible, non-parametric peak calling package for 4C and Capture-C data

Project description:High-resolution methods such as 4C and Capture-C enable the study of chromatin loops such as those formed between promoters and enhancers or CTCF/cohesin binding sites. An important aspect of 4C/CapC analyses is the identification of robust peaks in the data for the identification of chromatin loops. Here we present an R package for the analysis of 4C/CapC data. We generated 4C data for 10 viewpoints in 2 tissues in triplicate to test our methods. We developed a non-parametric peak caller based on rank-products. Sampling analysis shows that not read depth but template quality is the most important determinant of success in 4C experiments. By performing peak calling on single experiments we show that the peak calling results are similar to the replicate experiments, but that false positive rates are significantly reduced by performing replicates.

2018-05-14 | GSE105177 | GEO

Enhancer infestation drives tumorigenic activation of inactive compartment in Epstein-Barr virus-positive nasopharyngeal carcinoma [4C-Seq]

Project description:We detected the EBV interaction regions and the genomic loops from TSS of PLA2G4A in nasopharyngeal carcinoma cell lines by 4C-seq analysis.

2024-03-27 | GSE225247 | GEO

CTCF binding polarity determines chromatin looping [4C]

2015-10-29 | GSE72539 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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