Hemimethylation of CpG dyads is characteristic of secondary DMRs associated with imprinted loci and correlates with 5-hydroxymethylcytosine at paternally methylated sequences

Table 1 Comparison of dinucleotide content within primary vs. secondary DMRs (P values)

	CpG	GpC	ApT	TpA	ApA+ TpT	ApC+ GpT	ApG+ CpT	CpA+ TpG	CpC+ GpG	GpA+ TpC
Pat1° vs. Mat1°	0.0240	0.0139	0.0004	0.0444	0.4542	0.2515	0.9681	0.0074	0.0461	0.7065
Pat2° vs. Mat2°	0.4963	0.9369	0.9178	0.9987	0.3756	0.1281	0.2590	0.9287	0.7013	0.6743
Pat1° vs. Pat2°	0.0861	0.0835	0.0102	0.0387	0.2490	0.3482	0.6532	0.0768	0.0486	0.5086
Mat1° vs. Mat2°	0.7422	0.6371	0.7383	0.4821	0.6925	0.1175	0.2031	0.8800	0.9646	0.9638
Pat1° vs. Mat2°	0.1057	0.0472	0.0160	0.0218	0.7908	0.0570	0.2808	0.0187	0.1886	0.7569
Pat2° vs. Mat1°	0.5735	0.7343	0.8067	0.5679	0.4508	0.6926	0.6236	0.9804	0.6192	0.6434

(Pat1° paternally methylated primary DMR, Mat1° maternally methylated primary DMR, Pat2° paternally methylated secondary DMR, Mat2° maternally methylated secondary DMR. Frequency of each dinucleotide was determined as described in “Methods”. P values were calculated using a two-tailed t test for independent samples as described in “Methods”. Raw data are found in Additional file 3

ISSN: 1756-8935