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Table 6 Summary of changes in methylation during in vitro development for genome features

From: Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa

FEATURE

Explant to callus

Callus to regen

Whole genome (tiled windows)

+ 12%

- 22%

Intergenic spaces

- 3%

- 24%

Gene promoters

- 10%

- 27%

5’UTRs

- 48%

+ 324%

3’ UTRs

+ 8%

+ 86%

Gene bodies

+ 47%

- 44%

Transposable elements

+ 80%

+ 240%

  1. Data is changes in percent of genes called methylated by the negative binomial method at a false discovery rate of 10%. Calculated as: 100*[(Number of genes called in tissue 1 – number called in tissue 2) / mean number of genes called in tissue 1].