Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CAPTURE-3C-seq analysis of cis-element-mediated long-range DNA interactions

ABSTRACT: CAPTURE-3C-seq analysis of cis-element-mediated long-range DNA interactions

PROVIDER: PRJNA387464 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	SRR5583320.fastq.gz	Fastqsanger.gz
	SRR5583320_1.fastq.gz	Fastqsanger.gz
	SRR5583320_2.fastq.gz	Fastqsanger.gz
	SRR5583340.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 217

Similar Datasets

CAPTURE-3C-seq analysis of cis-element-mediated long-range DNA interactions

Project description:Cis-regulatory elements (CREs) are commonly recognized by correlative chromatin features, yet the molecular composition of the vast majority of CREs in chromatin remains unknown. Here we describe a CRISPR affinity purification in situ of regulatory elements (CAPTURE) approach to unbiasedly identify locus-specific chromatin-regulating protein complexes and long-range DNA interactions. Using an in vivo biotinylated endonuclease-deficient Cas9 protein and sequence-specific guide RNAs, we show high-resolution and selective isolation of chromatin interactions at a single copy genomic locus. Purification of human telomeres using CAPTURE identifies known and new telomeric factors. In situ capture of individual constituents of the enhancer cluster controlling human β-globin genes establishes evidence for composition-based hierarchical organization of enhancer structure. Furthermore, unbiased analysis of chromatin interactions at disease-associated cis-elements and developmentally controlled super-enhancers reveals spatial features causally regulate gene transcription. Thus, comprehensive analysis of locus-specific regulatory composition provides mechanistic insight into genome structure and function in development and disease.

2017-08-24 | GSE99174 | GEO

CAPTURE-3C-seq analysis of cis-element-mediated long-range DNA interactions in K562 and G1E-ER4 cells

Project description:CAPTURE-3C-seq analysis of cis-element-mediated long-range DNA interactions in K562 and G1E-ER4 cells

| PRJNA578398 | ENA

CAPTURE-3C-seq analysis of cis-element-mediated long-range DNA interactions in K562 and G1E-ER4 cells

Project description:The spatiotemporal control of 3D chromatin structure is fundamental for gene regulation, yet it remains challenging to obtain high-resolution chromatin interacting profiles at cis-regulatory elements (CREs) by chromatin conformation capture (3C)-based methods. Here, we describe the redesigned dCas9-based CAPTURE method for multiplexed, high-throughput and high-resolution analysis of locus-specific chromatin interactions. Using C-terminally biotinylated dCas9, endogenous biotin ligase and pooled sgRNAs, the new system enables quantitative analysis of the spatial configuration of a few to hundreds of enhancers or promoters in a single experiment, enabling systematic comparisons across CREs within and between gene clusters. We reveal the hierarchical structure of super-enhancers (SEs) and distinct modes of SE-gene interactions. Multiplexed capture of temporal dynamics of promoter-centric interactions establishes the instructive function of enhancer-promoter looping in transcriptional regulation during lineage differentiation. These applications illustrate the ability of multiplexed CAPTURE for decoding the organizational principles of genome structure and function.

2020-02-20 | GSE139109 | GEO

CoV 3'UTR cis-acting element interactome

Project description:Comparison of CoV 3'UTR cis-acting element interactome to link the cis-acting element to coronavirus replication by LC-MS/MS. The study is performed by in vitro-transcribed RNA followed by RNA-protein pull-down assay. In addition, the concluded results are decided by comparison between the biological processes derived from analysis of interactome and the replication efficiency.

2024-08-07 | MSV000095535 | MassIVE

CoV 3'UTR cis-acting element interactome

2024-08-06 | MSV000095522 | MassIVE

A Long-Range cis-Regulatory Element for Class I Odorant Receptor Genes

Project description:Individual olfactory sensory neurons express a single odorant receptor (OR) gene from either class I genes residing in a single cluster on a single chromosome or class II genes spread over multiple clusters on multiple chromosomes. Here, we identify an enhancer element for mouse class I genes, the J element, that regulates class I gene expression of a much larger number of genes and over a much greater genomic distance than known class II gene enhancers. Our data reveal an extraordinary long-range cis-regulatory element that governs the singular class I gene expression and has been phylogenetically preserved to retain a single cluster organization of class I genes in mammals.

2017-07-23 | GSE90700 | GEO

ETI dependent cis-element discovery using capture ATAC-seq.

Project description:ETI dependent cis-element discovery using capture ATAC-seq.

| PRJEB34952 | ENA

Unlinking a lncRNA from its associated cis element [Capture-C]

Project description:Capture-C using probes at the Cdkn1b promoter and the Lockd promoter Many long non-coding (lnc) RNAs are reported to regulate gene expression and protein functions. However, the proportion of lncRNAs with biological activities among the thousands expressed in mammalian cells is controversial. We studied Lockd (LncRNA downstream of Cdkn1b), a 434 bp polyadenylated lncRNA originating 4 kb 3â to the Cdkn1b gene. Heterozygous and homozygous deletion of the 25 kb Lockd locus reduced Cdkn1b transcription by approximately 35 and 70% respectively in a mouse erythroid cell line. In contrast, homozygous insertion of a polyadenylation cassette 80 bp downstream of the Lockd transcription start site reduced the entire lncRNA transcript level by > 90%, but had no effect on Cdkn1b transcription. The promoter of the Lockd gene contains a DNase hypersensitive site, binds numerous transcription factors (TFs), and physically associates with the Cdkn1b promoter in chromosomal conformation capture (NG Capture-C) studies. Thus, the Lockd gene positively regulates Cdkn1b transcription through an enhancer-like cis element, while the lncRNA itself is dispensable. These findings demonstrate that the biological activities of a lncRNA cannot be inferred from phenotypes that arise after deleting the corresponding gene. Rather, the model of an inert transcript arising from a functional genomic cis element should be considered while investigating the biology of any lncRNA.

2016-06-01 | E-GEOD-75880 | biostudies-arrayexpress

Chromosome conformation capture-on-chip analysis of long-range cis interactions of the SOX9 promoter

Project description:Transcription factor SOX9 is essential for the differentiation of chondrocytes and the development of testes. Heterozygous point mutations and genomic deletions involving SOX9 lead to campomelic dysplasia (CD) often associated with sex reversal. Chromosomal rearrangements with breakpoints mapping up to 1.3 Mb up- and downstream to SOX9, and likely disrupting its distant cis-regulatory elements, have been described in patients with milder forms of CD. Performing chromosome conformation capture-on-chip (4C) analysis in Sertoli cells and lymphoblasts we identified several novel potentially cis-interacting regions both up- and downstream to SOX9, with some of them overlapping lncRNA genes preferentially expressed in testes. Custom designed 3x720K tiling microarrays covering 4 Mb region (chr17:68,117,161-72,122,560) flanking SOX9 gene of interest

2013-09-08 | E-GEOD-50449 | biostudies-arrayexpress

CAPTURE-3C-seq analysis of locus-specific long-range DNA interactions in HeLa stable cells expressing LAMPS and sgHS2

Project description:We demonstrate that LAMPS-mediated LLPS induces the formation of long-range chromatin interactions

2023-03-16 | GSE180547 | GEO