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Chem-map: Profiling drug binding to chromatin in cells

ABSTRACT: Chem-map: Profiling drug binding to chromatin in cells

PROVIDER: PRJNA862136 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR20652900_1.fastq.gz	Fastqsanger.gz
	SRR20652900_2.fastq.gz	Fastqsanger.gz
	SRR20652901_1.fastq.gz	Fastqsanger.gz
	SRR20652901_2.fastq.gz	Fastqsanger.gz
	SRR20652902_1.fastq.gz	Fastqsanger.gz

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Chem-map profiles drug binding to chromatin in cells.

Project description:Characterizing drug-target engagement is essential to understand how small molecules influence cellular functions. Here we present Chem-map for in situ mapping of small molecules that interact with DNA or chromatin-associated proteins, utilizing small-molecule-directed transposase Tn5 tagmentation. We demonstrate Chem-map for three distinct drug-binding modalities as follows: molecules that target a chromatin protein, a DNA secondary structure or that intercalate in DNA. We map the BET bromodomain protein-binding inhibitor JQ1 and provide interaction maps for DNA G-quadruplex structure-binding molecules PDS and PhenDC3. Moreover, we determine the binding sites of the widely used anticancer drug doxorubicin in human leukemia cells; using the Chem-map of doxorubicin in cells exposed to the histone deacetylase inhibitor tucidinostat reveals the potential clinical advantages of this combination therapy. In situ mapping with Chem-map of small-molecule interactions with DNA and chromatin proteins provides insights that will enhance understanding of genome and chromatin function and therapeutic interventions.

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Chem-map: Profiling drug binding to chromatin in cells

Project description:We present a method of mapping binding sites of small molecules on chromatine targets in situ, in U2OS and K562 cell lines

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Chem-Seq of chemical derivatives in MM1S cells

Project description:An ability to map the global interactions of a chemical entity with chromatin genome-wide could provide new insights into the mechanisms by which a small molecule perturbs cellular functions. we developed a method that uses chemical derivatives and massively parallel DNA sequencing (Chem-Seq) to identify the sites bound by small chemical molecules throughout the human genome. We developed in vivo and in vitro Chem-Seq protocols with a biotinylated derivative of small molecules. In the in vivo protocol, Cells were first treated with biotinylated ligand and cross-linked with formaldehyde at the same time. Cells were then lysed, sonicated to shear the DNA, and streptavidin beads were used to isolate biotinylated ligand and associated chromatin fragments. We then used massively parallel sequencing to identify the enriched DNA fragments, and mapped these sequences to the genome. In in vitrol protocol, MM1.S cells were fixed and the derived sonicated lysate incubated with biotinylated drug to enrich for bound chromatin regions in vitro. We then used massively parallel sequencing to identify the enriched DNA fragments, and mapped these sequences to the genome.

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