Genome-wide methylation analysis demonstrates that 5-aza-2-deoxycytidine treatment does not cause random DNA demethylation in fragile X syndrome cells

Table 1 MS-MLPA analysis of the imprinted locus Prader–Willi/Angelman (PWS/AS) on chromosome 15 for WT, WT2, FXS1 and FXS2 before and after treatment with 5-azadC (1 µM) at three different time points (T1, T3 and T8)

Probes	WT1 UT ratio	WT1 T1 ratio	WT1 T3 ratio	WT1 T8 ratio
15-021.5 NDN	*0.48*	*0.30≪*	0.25≪	*0.59*
15-022.9 SNRPN	*0.56*	*0.43≪*	*0.51*	*0.48*
15-022.9 SNRPN	*0.57*	*0.35≪*	*0.41*	*0.45*
15-022.9 SNRPN	*0.58*	*0.31* ≪*	*0.36* ≪*	*0.5*
15-022.9 SNRPN	*0.41*	0.18	*0.3*	0.22
15-023.2 UBE3A Exon 1	0	0	0	0

Probes	WT2 UT ratio	WT2 T1 ratio	WT2 T3 ratio	WT2 T8 ratio
15-021.5 NDN	*0.48*	0.24≪	0	*0.37*
15-022.9 SNRPN	*0.52*	*0.4*	*0.47*	*0.61*
15-022.9 SNRPN	*0.52*	*0.39*	*0.44*	*0.55*
15-022.9 SNRPN	*0.5*	*0.36≪*	*0.47*	*0.57*
15-022.9 SNRPN	*0.41*	0.19≪	0.26	*0.32*
15-023.2 UBE3A exon 1	0	0	0	0

Probes	FXS1 UT ratio	FXS1 T1 ratio	FXS1 T3 ratio	FXS1 T8 ratio
15-021.5 NDN	*0.36*	0.25≪	0.28≪	*0.47*
15-022.9 SNRPN	*0.53*	*0.35*	*0.44*	*0.54*
15-022.9 SNRPN	*0.51*	*0.3*	*0.41*	*0.59*
15-022.9 SNRPN	*0.55*	*0.33<*	*0.39*	*0.53*
15-022.9 SNRPN	*0.4*	0.14≪	0.15≪	0.25
15-023.2 UBE3A exon 1	0.06	0.02	0.04	0.04

Probes	FXS2 UT ratio	FXS2 T1 ratio	FXS2 T3 ratio	FXS2 T8 ratio
15-021.5 NDN	*0.48*	*0.31≪*	0.26≪	*0.48*
15-022.9 SNRPN	*0.48*	*0.37*	0.5	*0.34*
15-022.9 SNRPN	*0.39*	*0.45*	0.48	*0.55*
15-022.9 SNRPN	0.2	*0.41*	0.42	*0.43*
15-022.9 SNRPN	0.13	0.26	0.19	0.17
15-023.2 UBE3A exon 1	0.06	0.14≪	0	0

Only methylation-sensitive probes are listed
Note that the asterisks indicate that the magnitude of the probe ratio exceed the set of arbitrary border values. The italic values represent levels of methylation lower than 30 %, while bold italic values represent those between 30 and 70 %

ISSN: 1756-8935