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 sitesa | Number of diff. meth. sites within features | ||||
|---|---|---|---|---|---|---|---|
| Annotated region | Not-annotated region | Gene-associated region | |||||
| Hypo- | Hyper- | Gene | Promoterb | ||||
| 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