I suggest to check this paper, specifically the methodology for ChIP to determine the methylation pattern for the genes studied with and without pathogen interaction.

Regards

Thanks Aaron, but this papers tells about histone methylation, we are mainly interested to look at DNA methylation. The technique in the above paper will not help us, will it?

Sachin, are the genomic size of the genes 6 kb? If so, there should not be a problem amplifying the whole region using specific primers and DNA polymerases specific for long templates.

I have sequenced PCR fragments before without any problem, many times. The only requirement is that the amplification is clean and there is absence of non-specific amplicons. Many polymerases are error prone, just like Taq, but since the errors are at random, there should not be a problem for sequencing, since the resulting analysis of the sequence will produce peaks of the most frequent base in each position.

If the genes are that small, I would recommend treating the DNA and amplifying each region with specific primers, focusing more on the core promoter regions (around 500 bp before transcription start site). For sequencing you would use the amplicons and need to design internal primers for sequencing with enough overlaps for producing sequences 600-700 long (some equipment could do 1000 pb of good sequences in ideal conditions) from both forward and reverse directions. The sequences will let you know if the base in the genomic DNA was a C or a T.