CpG methylation accounts for a recurrent mutation (c.1222C>T) in the human PAH gene

Area of Science:

• Genetics
• Molecular Biology
• Human Disease Genetics

Background:

• The human PAH gene contains alleles associated with hyperphenylalaninemia and phenylketonuria (PKU).
• The c.1222C>T allele (p.R408W) is the most common PKU-causing mutation, occurring on various haplotypes.
• The recurrence of this mutation is hypothesized to be due to methylation-mediated deamination of 5-methylcytosine (5mC) in CpG dinucleotides within hypermutable codons.

Purpose of the Study:

• To confirm the methylation status of the c.1222C nucleotide in the human PAH gene.
• To investigate the presence and distribution of 5-methylcytosine (5mC) in hypermutable codons of the PAH gene.
• To explore the evolutionary conservation of this methylation pattern in primates.

Main Methods:

• Analysis of PAH gene alleles and haplotypes.
• Confirmation of nucleotide methylation status in human somatic cells (leukocytes and brain).
• Examination of 5-methylcytosine distribution in specific regions (exons 12 and 7) of the human PAH gene.
• Comparative analysis of PAH gene methylation patterns in nonhuman primates.

Main Results:

• The c.1222C nucleotide in the human PAH gene is confirmed to be methylated (c.1222 mC) in somatic genomes.
• 5-methylcytosine (5mC) is localized specifically to cytosines within CpG dinucleotides in hypermutable codons of PAH exons 12 and 7.
• The observed PAH gene methylation pattern in humans is conserved in the corresponding codons of three nonhuman primate species.

Conclusions:

• The methylation of the PAH c.1222C nucleotide provides a molecular mechanism for the high frequency of the c.1222C>T (p.R408W) PKU allele.
• The findings support the concept of recurrent mutations arising from methylation-mediated deamination in hypermutable CpG sites.
• The evolutionary conservation of this methylation pattern suggests its functional significance in PAH gene evolution and disease association.