Provided are methylcytosine-selective deaminases, compositions, kits, and methods employing them, including a sequencing method involving (a) contacting
a DNA substrate comprising
cytosine (C) and at least one methylcytosine
nucleobase selected from 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) or comprising C and both 5mC and 5hmC, with a methylcytosine-selective deaminase to produce a
deamination product, wherein the methylcytosine-selective deaminase (i) is capable of deaminating 5mC to
thymidine (T) and / or 5hmC to hydroxymethyluridine (hmll) and (ii) preferentially deaminates the at least one methylcytosine
nucleobase relative to
cytosine (C); and (b) sequencing the
deamination product, or amplifying the
deamination product to produce an amplification product, and sequencing the amplification product, in each case, to produce sequence reads, wherein positions of Cs and position of the at least one methylcytosine
nucleobase in the
DNA substrate is determined based on the sequence reads.