3.1.1. FOXP3 TSDR methylation profile
CpG sites within TSDR of FOXP3 gene were analysed at both DNA
directions (forward and reverse DNA strands) and revealed a clear
deviation of methylation pattern between them. Among FA and control
samples, FOXP3 TSDR CpGs showed almost 100% methylation across
forward strand and a variable demethylation rate in the reverse strand
(Figure 2A), indicating that only reverse DNA strand methylation pattern
accounts for the gene’s transcriptional regulation.
FOXP3 gene is located on human chromosome X (Xp11.23) and
consequently, epigenetic discrepancies between different sexes may arise
from the inactivation process of X chromosome in females. To avoid
artifacts during methylation data analysis, male and female donors (both
controls and food allergic children) were analysed independently,
however insignificant gender differences were observed in methylation
profiles (data not shown).
Subsequent analysis revealed marginal variations (Figure 2B) in food
allergic children compared to controls. Also, the average methylation
level of all TSDR CpG sites tested was not statistically significant
between food allergic children and control groups, providing poor
evidence for the TSDR demethylation.