Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

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

PROVIDER: PRJNA1080212 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR28086969_1.fastq.gz	Fastqsanger.gz
	SRR28086969_2.fastq.gz	Fastqsanger.gz
	SRR28086970_1.fastq.gz	Fastqsanger.gz
	SRR28086970_2.fastq.gz	Fastqsanger.gz
	SRR28086971_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 26

Similar Datasets

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

Mycobacterium triplex

Project description:Mycobacterium triplex overview

| PRJNA247427 | ENA

Mycobacterium triplex

Project description:Mycobacterium triplex genome

| PRJEB5744 | ENA

The LncRNA Fendrr Regulates Lung Development via its Triplex Forming Site the Expression of Fibrosis Genes

Project description:Long non-coding RNAs are a very versatile class of molecules that have important roles in regulating a cells function, including regulating other genes on the transcriptional level. One of these mechanisms is that RNA can directly interact with DNA by recruiting additional components such as proteins to these sites via a RNA:dsDNA triplex formation. We genetically deleted the triplex forming sequence from the lncRNA Fendrr in mice and find that this FendrrBox is partially required for Fendrr function. we We find that the loss of the triplex forming site in developing lungs causes a dysregulation of gene programs, associated with lung fibrosis. Deregulated genes that contain a FendrrBox binding element in their promoter are regulated by Wnt signaling, together with Fendrr, implicating that Fendrr acts in concert with Wnt signaling to regulate lung fibrosis.

2023-04-30 | GSE186703 | GEO

Mycobacterium triplex

Project description:Whole genome sequencing of Mycobacterium triplex, an opportunistic pathogen

| PRJDB2636 | ENA

Geastrum triplex strain:GST.BST

Project description:Geastrum triplex strain:GST.BST Genome sequencing

| PRJNA256707 | ENA

PPIA-mediated stabilization of GAU1-SENP5 triplex activates the oncogene SENP5 drives tumorigenesis

Project description:All DNA interacting with GAU1 lncRNA were detected by triplex

2024-07-28 | GSE247292 | GEO

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

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 | GSE120848 | 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