Plant-RRBS, a bisulfite and next-generation sequencing-based methylome profiling method enriching for coverage of cytosine positions

Table 3 Differential cytosine methylation and annotation of the control line versus the LR2 epiline (fourth selfing)

Restriction endonuclease combination	Cytosine site	Number of differentially methylated sites^a		Number of diff. meth. sites within features
		Number of differentially methylated sites^a		Annotated region	Not-annotated region	Gene-associated region
		Hypo-	Hyper-	Annotated region		Gene	Promoter^b
MspI-ApeKI	CG	541	463	182	822	160	362
	CHG	169	94	28	235	28	81
	CHH	20	8	11	17	4	4
	sum	730	565	221	1074	192	447
MspI-DpnII	CG	29	74	9	94	8	27
	CHG	10	25	0	35	0	11
	CHH	2	2	1	3	1	0
	sum	41	101	10	132	9	38

Cytosine positions, represented by the numbers above, can be counted to the different annotations multiple times
^a hypo−/hyper-methylated means a 25% lower/higher methylation level in LR2 compared with the control line
^b Promoter is defined as 2000 nucleotides upstream of the TSS and belongs to the not-annotated region in the used genomic features

ISSN: 1471-2229