MeTS relevant blood methylome signatures

We have searched for methylome differences between the whole blood (WB) of 3-year-old girl diagnosed due to delayed psychomotor development and short stature, and the WB sample of 45 years old man being the father and also such of 43 years old women being the mother of the mentioned child. We have generated differentially methylated data sets for CpG enriched portions of the three investigated WB genomes using reduced representation bisulfite sequencing approach (RRBS). MspI digested DNA prepared from whole blood were ligated to methylated adapters and size selected to obtain CpG enriched fraction of genomic DNA, which were further bisulfite converted and PCR amplified. RRBS libraries were sequenced in 75bp single end read on the NextSeq 550 system (Illumina). Applied RRBS approach showed the presence of 10250 differentially methylated CpG sites (DMS) where 4048 were hypo- and 6202 were hypermethylated in the WB genome of the girl in reference to the parental WB samples. Genomic annotation of identified DMS sites resulted in the collection of genes of bivariate methylation state which were overrepresented in cell adhesion and cell junction relevant biological processes. Such as those encoded cadherins and phospho- and calcium related proteins. Among them large groups were genes encoding phosphoproteins involved in metabolic, immune-, calcium- and insulin signalling pathways. Exclusively hypermethylated genes formed an overrepresented set of encoded proteins being components of neuromuscular junctions. Hypermethylation of parental blood samples in relation to the blood of diagnosed child was also associated with overrepresentation of genes encoding proteins involved in chromosomal rearrangement and mental retardation.