Preservation of information related to genomic DNA methylation

A method of identifying methylated cytosines in a plurality of nucleic acids, said method comprising:

• providing a sample comprising a plurality of template nucleic acids;
• generating complementary copies of said template nucleic acids, said generating being directed by an oligonucleotide primer using a nucleic acid polymerase in the presence of a bisulfite-resistant cytosine analog, wherein said generating produces a complementary copy of each of said template nucleic acids such that cytosine residues in each of said complementary copy are bisulfite-resistant, and wherein each complementary copy is coupled to one of said template nucleic acids;
• subjecting said template nucleic acids and said complementary copies to bisulfite treatment to convert unmethylated cytosine residues in said template nucleic acids into uracil residues, resulting in each bisulfite-converted template nucleic acid being coupled to a non-converted complementary copy;
• determining the nucleotide sequence of said bisulfite-converted template nucleic acids and said non-converted complementary copies;
• and
• comparing said nucleotide sequence of said bisulfite-converted template nucleic acids to the nucleotide sequence of said non-converted complementary copies for each of said bisulfite-converted template nucleic acids coupled to non-converted complementary copies, thereby determining the methylation status of the template nucleic acids prior to bisulfite conversion.