Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Detection of RNA–DNA binding sites in long noncoding RNAs

ABSTRACT: Triple helix is a potential mechanism how lncRNAs interact with the genome. Our in silico method (Triplex Domain Finder) is able to predict the binding sites of lncRNA MEG3 and GATA6-AS in the genome. In order to validate these predictions, we develop DBD-Capture-Seq to capture the DNA loci where the given RNA oligo binds to via triplex. Method: Different RNA oligos are used The biotinylated RNA oligos (MEG3 TFR1, MEG3 TFR2, and GATA6-AS TFR1) were incubated with sheared genomic DNA to allow for triplex formation. After binding to streptavidin-coated beads, RNA-associated DNA was eluted and subjected to deep sequencing. Control experiments were conducted in the absence of biotinylated RNA oligos.

ORGANISM(S): Homo sapiens

PROVIDER: GSE119638 | GEO | 2019/01/15

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

ChIRP-MS dataset generated from Peptidylprolyl isomerase A guides SENP5/GAU1 DNA-lncRNA triplex generation for driving tumorigenesis

Project description:The three-stranded DNA-RNA triplex hybridization is involved in various biological processes, including gene expression regulation, DNA repair, and chromosomal stability. However, the DNA-RNA triplex mediating mechanisms underlying tumorigenesis remain to be fully elucidated. In gastric cancer, we performed ChIRP-MS in order to further capture the trimer-forming lncRNA binding protein.

2024-09-20 | PXD056041 | Pride

Interacting proteins of the NRAS RNA G-quadruplex

Project description:Biotinylated RNA oligos were used as baits for affinity enrichments from cytoplasmic cell extracts.

2019-11-12 | PXD010860 | Pride

Chemoproteomic profiling unveils binding and functional diversity of endogenous proteins that interact with endogenous triplex DNA

Project description:Triplex DNA structures, formed by a third DNA strand wrapped around the major groove of double helix, are key molecular regulators and genomic threats that are pharmacologically exploitable. However, the regulatory network governing triplex DNA dynamics are poorly understood. Here we performed chemoproteomic profiling of triplex DNA interactome in live cells to address this knowledge gap. We developed and validated a chemical probe that exhibits exceptional specificity for recognizing triplex DNA structures. By employing a co-binding-mediated proximity capture strategy, we enriched triplex DNA interactome for quantitative proteomics analysis. This enabled the identification of a comprehensive list of triplex DNA interacting proteins, characterized by diverse binding properties and regulatory mechanisms in native chromatin context. As a demonstration, we further validated DDX3X as the first ATP-independent helicase capable of resolving triplex DNA structures with 5' overhangs on the third DNA strand to prevent triplex-DNA-induced DNA damages. Overall, our triplex DNA interactome offers a valuable resource for investigating the biology of triplex DNA in both health and disease.

2024-07-17 | GSE257561 | GEO

Meg3 binding sites in mouse insulinoma cells

Project description:We have shown that increased β-cell proliferation in functioning pancreatic neuroendocrine tumors (insulinomas) correlated with reduced expression of the long non-coding RNA Meg3 and increased expression of the oncogenic receptor c-Met. To investigate the target binding sites of Meg3 in and around the c-Met gene, we did ChIRP-Seq using biotinylated probes from the mouse Meg3 RNA sequence. This would help us better understand how Meg3 regulates ithe expression of c-Met to control β-cell proliferation in insulinoma cells.

2017-09-20 | GSE99798 | GEO

MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA–DNA triplex structures

Project description:MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA–DNA triplex structures

| PRJEB7307 | ENA

The long non-coding RNA Meg3 mediates imprinted gene expression during stem cell differentiation

Project description:The imprinted Dlk1-Dio3 domain comprises the developmental genes Dlk1 and Rtl1, which are silenced on the maternal chromosome in different cell types. On this parental chromosome, the domain’s imprinting control region activates a polycistron that produces the lncRNA Meg3 and many miRNAs (Mirg) and C/D-box snoRNAs (Rian). Although Meg3 lncRNA is nuclear and associates with the maternal chromosome, it is unknown whether it controls gene repression in cis. We created mouse embryonic stem cells (mESCs) that carry an ectopic poly(A) signal, reducing RNA levels along the polycistron, and generated Rian-/- mESCs as well. Upon ESC differentiation, we found that Meg3 lncRNA (but not Rian) is required for Dlk1 repression on the maternal chromosome. Biallelic Meg3 expression acquired through CRISPR-mediated demethylation of the paternal Meg3 promoter led to biallelic Dlk1 repression, and to loss of Rtl1 expression. lncRNA expression also correlated with DNA hypomethylation and CTCF binding at the 5’-side of Meg3. Using Capture Hi-C, we found that this creates a Topologically Associating Domain (TAD) organization that brings Meg3 close to Dlk1 on the maternal chromosome. The requirement of Meg3 for gene repression and TAD structure may explain how aberrant MEG3 expression at the human DLK1-DIO3 locus associates with imprinting disorders.

2024-03-28 | GSE207166 | GEO

Isolation and genome-wide characterization of cellular DNA:RNA triplex structures IV

Project description:RNA can directly bind to purine-rich DNA via Hoogsteen base pairing, forming a DNA:RNA triple helical structure that anchors the RNA to specific sequences and allows guiding of transcription regulators to distinct genomic loci. To unravel the prevalence of DNA:RNA triplexes in living cells, we have established a fast and cost-effective method that allows genome-wide mapping of DNA:RNA triplex interactions. In contrast to previous approaches applied for the identification of chromatin-associated RNAs, this method uses protein-free nucleic acids isolated from chromatin. High-throughput sequencing and computational analysis of DNA-associated RNA revealed a large set of RNAs which originate from non-coding and coding loci, including repeat elements. Combined analysis of DNA-associated RNA and RNA-associated DNA identified genomic DNA:RNA triplex structures. The results suggest that triplex formation is a general mechanism of RNA-mediated target-site recognition, which has major impact on biological functions.

2018-12-20 | GSE120849 | GEO

Isolation and genome-wide characterization of cellular DNA:RNA triplex structures II

2018-12-20 | GSE120846 | GEO

Isolation and genome-wide characterization of cellular DNA:RNA triplex structures I

2018-12-20 | GSE120845 | GEO

Isolation and genome-wide characterization of cellular DNA:RNA triplex structures III

2018-12-20 | GSE120848 | GEO