Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA duplex map in living cells reveals higher order transcriptome structure

ABSTRACT: RNA duplex map in living cells reveals higher order transcriptome structure

PROVIDER: PRJNA299809 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR2814761.fastq.gz	Fastqsanger.gz
	SRR2814762.fastq.gz	Fastqsanger.gz
	SRR2814763.fastq.gz	Fastqsanger.gz
	SRR2814764.fastq.gz	Fastqsanger.gz
	SRR2814765.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 14

Similar Datasets

RNA duplex map in living cells reveals higher order transcriptome structure

Project description:RNA has the intrinsic property to base pair, forming complex structures fundamental to its diverse functions. Here we develop PARIS, a method based on reversible psoralen-crosslinking for global mapping of RNA duplexes with near base-pair resolution in living cells. PARIS analysis in three human and mouse cell types reveals frequent long-range structures, higher order architectures, and RNA:RNA interactions in trans across the transcriptome. PARIS determines base-pairing interactions on an individual-molecule level, revealing pervasive alternative conformations. We used PARIS-determined helices to guide phylogenetic analysis of RNA structures, and discovered conserved long-range and alternative structures. XIST, a lncRNA essential for X chromosome inactivation, folds into evolutionarily conserved RNA structural domains that span many kilobases. XIST A-repeat forms complex inter-repeat duplexes that nucleate higher order assembly of the key epigenetic silencing protein SPEN. PARIS is a generally applicable and versatile method that provides novel insights into the RNA structurome and interactome. Cells are crosslinked with AMT and RNA is extracted from cells by RNase digestion. Crosslinked RNA fragments are selected from total RNA by 2D gel electrophoresis. Purified crosslinked RNA duplexes are proximity ligated and crosslinking is reversed. Then the chimeric RNA molecules are converted into cDNA libraries for high-throughput sequencing.

2016-04-04 | E-GEOD-74353 | biostudies-arrayexpress

RNA duplex map in living cells reveals higher order transcriptome structure

2016-04-04 | GSE74353 | GEO

RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure.

Project description:RNA has the intrinsic property to base pair, forming complex structures fundamental to its diverse functions. Here, we develop PARIS, a method based on reversible psoralen crosslinking for global mapping of RNA duplexes with near base-pair resolution in living cells. PARIS analysis in three human and mouse cell types reveals frequent long-range structures, higher-order architectures, and RNA-RNA interactions in trans across the transcriptome. PARIS determines base-pairing interactions on an individual-molecule level, revealing pervasive alternative conformations. We used PARIS-determined helices to guide phylogenetic analysis of RNA structures and discovered conserved long-range and alternative structures. XIST, a long noncoding RNA (lncRNA) essential for X chromosome inactivation, folds into evolutionarily conserved RNA structural domains that span many kilobases. XIST A-repeat forms complex inter-repeat duplexes that nucleate higher-order assembly of the key epigenetic silencing protein SPEN. PARIS is a generally applicable and versatile method that provides novel insights into the RNA structurome and interactome. VIDEO ABSTRACT.

| S-EPMC5029792 | biostudies-literature

SETMAR regulates gene expression and modulates higher order chromatin structure

Project description:SETMAR regulates gene expression and modulates higher order chromatin structure

| PRJNA642400 | ENA

DNA methylation maintains integrity of higher order genome architecture

Project description:DNA methylation maintains integrity of higher order genome architecture

| PRJNA663616 | ENA

Higher-Order Organization Principles of Pre-translational mRNPs [RIPPLiT]

Project description:Higher-Order Organization Principles of Pre-translational mRNPs [RIPPLiT]

| PRJNA476057 | ENA

Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations

Project description:Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations

| PRJNA1083585 | ENA

Genetic Evidence for Asymmetric Blocking of Higher-Order Chromatin Structure by CTCF/Cohesin

Project description:Genetic Evidence for Asymmetric Blocking of Higher-Order Chromatin Structure by CTCF/Cohesin

| PRJNA560861 | ENA

SMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells

Project description:The packaging of DNA into chromatin plays an important role in transcriptional regulation and nuclear processes. Brahma related gene-1 SMARCA4 (also known as BRG1), the essential ATPase subunit of the mammalian SWI/SNF chromatin remodeling complex, uses the energy from ATP hydrolysis to disrupt nucleosomes at target regions. Although the transcriptional role of SMARCA4 at gene promoters is well-studied, less is known about its role in higher-order genome organization. SMARCA4 knockdown in human mammary epithelial MCF-10A cells resulted in 176 up-regulated genes, including many related to lipid and calcium metabolism, and 1292 down-regulated genes, some of which encode extracellular matrix (ECM) components that can exert mechanical forces and affect nuclear structure. ChIP-seq analysis of SMARCA4 localization and SMARCA4-bound super-enhancers demonstrated extensive binding at intergenic regions. Furthermore, Hi-C analysis showed extensive SMARCA4-mediated alterations in higher-order genome organization at multiple resolutions. First, SMARCA4 knockdown resulted in clustering of intra- and inter- sub-telomeric regions, demonstrating a novel role for SMARCA4 in telomere organization. SMARCA4 binding was enriched at TAD (Topologically Associating Domain) boundaries, and SMARCA4 knockdown resulted in weakening of TAD boundary strength. Taken together, these findings provide a dynamic view of SMARCA4-dependent changes in higher-order chromatin organization and gene expression, identifying SMARCA4 as a novel component of chromatin organization. Hi-C and RNA-seq experiments were conducted in MCF-10A shSCRAM and shSMARCA4 cells. SMARCA4 ChIP-seq was conducted in wildtype MCF-10A cells.

2016-06-02 | E-GEOD-74716 | biostudies-arrayexpress

Co-opted transposons help perpetuate conserved higher-order chromosomal structures

Project description:Co-opted transposons help perpetuate conserved higher-order chromosomal structures

| PRJNA593858 | ENA