DamID principle
DamID is a method that identifies genomic binding sites of a protein of interest (POI). In contrast to ChIP-seq, no antibodies against the POI are required.
The method is based on fusing the POI to a DNA adenine methyltransferase (Dam) from E. coli. Dam methylates adenine bases in GATC motifs, which are not present in the eukaryotic genome.
To identify the genomic binding sites of the POI, the Dam-fusion protein is expressed in cells. Over time, the Dam-fusion protein will bind to the chromatin and methylate the GATC motifs in the vicinity of the binding sites. These methylation marks effectively function as a recording of the history of the chromatin binding of the POI.
For quantification, DNA is isolated and methylated DNA is cloned and subsequently sequenced.
Figure adapted from Van den Ameele et al. 2019 Current Opinion in Neurobiology
Experimental considerations
Make sure that you have sequence validated your Dam expressing plasmids prior to your experiment. Cryptic expression of Dam can cause toxicity in E. coli and can cause selection for Dam inactivating mutations.