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

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

PROVIDER: PRJNA494707 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7965700.fastq.gz	Fastqsanger.gz
	SRR7965701.fastq.gz	Fastqsanger.gz
	SRR7965702.fastq.gz	Fastqsanger.gz
	SRR7965703.fastq.gz	Fastqsanger.gz
	SRR7965704.fastq.gz	Fastqsanger.gz

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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.

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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.

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

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