Detection of methylation in promoter sequences by melting curve analysis-based semiquantitative real time PCR

The promoters of the RASSF1A (3p21.3), BLU (3p21.3) and MGMT (10q26) genes were analyzed by MCA-MSP and MCA-Meth in 13 astrocytoma samples, 6 high grade glioma cell lines and 4 neuroblastoma cell lines. The data were compared with standard MSP and validated by bisulfite sequencing.Both, MCA-MSP and MCA-Meth, successfully determined promoter methylation. MCA-MSP provided information similar to standard MSP analyses. However the analysis was possible in a single tube and avoided the gel stage. MCA-Meth proved to be useful in samples with intermediate methylation status, reflected by a melting curve position shift in dependence on methylation extent.We propose MCA-MSP and MCA-Meth as alternative or supplementary techniques to MSP or bisulfite sequencing.DNA methylation in promoter regions has a regulatory effect on gene transcription. The conversion by covalent binding of a methyl residue from cytosine to 5-methylcytosine (m5C) at CpG dinucleotides occurs in both, prokaryotic and eukaryotic genomes and represents the most abundant methylated base in the genome of vertebrates. Areas of high CpG dinucleotide density, so called "CpG islands", are spread throughout the genome and usually map to gene promoter regions. Almost half of the genes in our genome have such CpG-rich promoter regions [1]. Methylation of CpG islands is associated with histone deacetylation and transcriptional silencing [2] and it is essential for normal embryonic development, genomic imprinting and X-chromosome inactivation. It also plays a role in cancer, as tumor suppressor gene promoter methylation leads to their inactivation.In standard PCR and cloning procedures, information about m5C and other covalent base modifications in genomic DNA is lost. Therefore, PCR methods for detecting and mapping m5C in specific genes rely on treatment of genomic DNA with methylation-sensitive restriction endonucleases or sodium bisulfite treatment before amplification. A specific target sequence can subsequently b