A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands.

TLDR

The modulation of DNA‑protein interactions by methylation and the distinct methylation patterns seen in genomic imprinting, X‑chromosome inactivation, and fragile X syndrome underscore the need to map methylation on individual DNA strands. We report a genomic sequencing method that positively identifies 5‑methylcytosine residues and yields strand‑specific sequences of individual genomic DNA molecules. The method employs bisulfite conversion that turns cytosine into uracil while leaving 5‑methylcytosine unchanged, followed by strand‑specific PCR amplification and sequencing (directly or after cloning) to produce strand‑specific methylation maps, as demonstrated on CpG sites in the human kininogen promoter. The technique revealed an atypical methylation pattern in sperm DNA, suggesting that high methylation of single‑copy sequences may be locally modulated by protein‑binding factors in germ‑line cells.

Abstract

The modulation of DNA-protein interactions by methylation of protein-binding sites in DNA and the occurrence in genomic imprinting, X chromosome inactivation, and fragile X syndrome of different methylation patterns in DNA of different chromosomal origin have underlined the need to establish methylation patterns in individual strands of particular genomic sequences. We report a genomic sequencing method that provides positive identification of 5-methylcytosine residues and yields strand-specific sequences of individual molecules in genomic DNA. The method utilizes bisulfite-induced modification of genomic DNA, under conditions whereby cytosine is converted to uracil, but 5-methylcytosine remains nonreactive. The sequence under investigation is then amplified by PCR with two sets of strand-specific primers to yield a pair of fragments, one from each strand, in which all uracil and thymine residues have been amplified as thymine and only 5-methylcytosine residues have been amplified as cytosine. The PCR products can be sequenced directly to provide a strand-specific average sequence for the population of molecules or can be cloned and sequenced to provide methylation maps of single DNA molecules. We tested the method by defining the methylation status within single DNA strands of two closely spaced CpG dinucleotides in the promoter of the human kininogen gene. During the analysis, we encountered in sperm DNA an unusual methylation pattern, which suggests that the high methylation level of single-copy sequences in sperm may be locally modulated by binding of protein factors in germ-line cells.