DamID – Mapping Protein-Genome Interactions

Scientists at the Fred Hutchinson Cancer Research Center, The Netherlands Cancer Institute (NKI) and Cancer Research Technology Limited (CRT) have released details of the development and commercialisation of a protein-genome interaction mapping technology termed ‘DamID.’

DamID maps protein-genome interactions using tethered DNA adenine methyltransferase to create unique tags, which mark binding sites. This novel technology addresses current limitations of existing techniques to identify in vivo genome binding sites of proteins.

Technology

DamID is based on the creation of a fusion protein consisting of Escherichia coli DNA adenine methyltransferase (Dam) and the chromatin protein or transcription factor of interest. Dam methylates adenines in the sequence GATC, an event that does not occur naturally in most eukaryotes. Upon expression of the fusion protein in cultured cells or in an intact organism such as Drosophila, the protein of interest targets Dam to the native DNA binding sites of the protein. This results in the sequence specific local methylation of adenine residues (Figure 1). Subsequent screening for methylated adenines using a sensitive microarray-based readout identifies sequences that were bound by the chromatin protein or transcription factor of interest. When genomic tiling arrays are used, maps of protein binding can be obtained with an approximate resolution of 1kb, thus allowing the construction of transcriptional regulatory networks. A PCR based detection method is also available to probe targeted methylation of individual genomic loci.

What it does

• Identifies protein-genome interactions in living cells and whole organisms
• Suitable for studying novel DNA binding proteins as no antibody is required
• Identifies direct and indirect interactions between protein and DNA targets
• Validated in multiple species and cell types

This efficient large-scale mapping technology has been validated in multiple cell types, and has direct application in the fields of transcription, DNA replication, chromatin
modelling, chromosome segregation and genome maintenance. DamID has been successfully applied to studying chromatin-associated proteins in Drosophila and
mammalian genomes. CRT is seeking a partner to make this technology available to the research community.

Which proteins can be studied using DamID?

DamID has been shown to work well for proteins that interact either directly or indirectly (through other proteins) with target DNA sequences in Drosophila (cultured cells or intact flies) and mammalian cells.