Is there any direct method of studing methylation. Is there any modified nucleotide which can bind specifically to methylated Nucleotide? Do not want to do bisulfide sequencing. Is there any other way to find methylation?
Note, that some commonly used methods can't distinguish between 5-methylcytosine and 5-hydroxymethylcytosine: both modified nucleotides will be seen as 5-methylcytosine (Nestor et al., 2010). For precise analysis using of highly specific antibodies or methylcytosine/hydroxymethylcytosine-binding proteins is recommended (Nomura et al., 2011; Booth et al., 2012).
If you know the specific region that you wish to analyze, there are approaches like that described here:
http://www.zymoresearch.com/epigenetics/dna-methylation/region-specific-dna-methylation-analysis/onestep-qmethyl-kit