Table 1.

Methylation analysis

	pFC19				pCLH22
	SNRPN		EBNA1		Luciferase		EBNA1
	3a	3a + 3L	3a	3a + 3L	3a	3a + 3L	3a	3a + 3L
me-CpG	101	418	103	211	83	246	142	387
n	53	53	37	35	44	32	34	60
Methylation, %	8.3	34.3	27.5	54.8	6.7	27.5	38	58.6
Fold stimulation		4.1		2.0		4.1		1.5

Regions of the SNRPN IC (carried by pFC19) or the luciferase gene (carried by pCLH22) were analyzed for methylation by the bisulfite sequencing method. For both episomes, a region of the neighboring EBNA1 gene was also analyzed. The number of methylated CpG sites observed for each region (me-CpG) and the sample size (n) are included in each column. The efficiency of CpG methylation (% methylation) is calculated by dividing the number of methylated sites observed by the total number of CpG sites in each region. The fold stimulation corresponds to the ratio of the efficiency observed when Dnmt3a and DNMT3L were expressed together relative to the efficiency observed when Dnmt3a was expressed alone. Note that molecules carrying nonconverted cytosines at non-CpG sites were excluded from the analysis. Such molecules were observed at low frequencies (3/106) only for the SNRPN region.