Question

One of the first genomic methods to study nuclear organization genome-wide was DamID, which was first carried out using lamin B1 DamID. Typically DamID results are normalized by using a ratio of the signal produced by the Dam methylase fused to the target protein (in this case lamin B1) divided by the signal produced by free Dam methylase.

Why is this ratio used?  What does the ratio correct for?

Answer 1

In these assays to study genome wide association, Dam methylase is used as a marker to identify sites where the target protein associates with the genome. At all loci where the target protein associates with DNA, Dam methylates the site, which is later identified.

However the methylation of any locus could also be due to the action of Dam methylase alone, without the target protein associating with the genome. Therefore a ratio is used to correct for the sites that are modified due to the activity of Dam methylase alone, without the target protein being involved.