Chem-seq

Mapping the global interactions of these chemical entities with chromatin in a genome-wide manner could provide insights into the mechanisms by which a small molecule influences cellular functions.

In a broader sense, these methods will be useful to enhance our understanding of the therapeutic mechanisms through which small molecules modulate the function and activity of genome-associated proteins.

DNA is then extracted from the cells, sonicated and enriched for regions containing the biotinylated molecule of interest by incubation with streptavidin magnetic beads, which have a very high affinity for biotin.

Chem-seq was tested on three classes of drugs using MM1.S multiple myeloma cells to:[1] 1) Investigate the genome-wide binding of the bromodomain inhibitor JQ1 to the BET bromodomain family members BRD2, BRD3 and BRD4 2) Map the genomic binding sites of AT7519, an inhibitor of the cyclin dependent kinase CDK9, and 3) Study how the DNA intercalating agent psoralen interacts with genomic DNA in vivo.

It can be used in conjunction with ChIP-seq to cross reference the location of certain drugs with DNA binding proteins, like transcription factors, to discover novel interactions and aid in characterizing the molecular mechanisms through which small molecules affect the genome.

Previously, another similar technique known as chromatin affinity-precipitation (ChAP) assay was used to map the sites of interaction of metabolic compounds in the yeast genome,[4] but Chem-seq is the first method to assess the genome-wide localization of small molecules in mammalian cells.