Table 1 Validation of the NGS profiles.

From: DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation

Sequence

Rank in NNCGNN profile

Relative methylation (mean ± SD)

GTACGTAA

1

3.77 ± 0.50

TTCCGTAA

2

4.32 ± 0.43

TCCCGGAA

170

1.0

TCGCGAGC

254

0.36 ± 0.03

TCGCGAGA

254

0.33 ± 0.04

  1. NGS derived flanking sequence preferences were validated by radioactive DNA methylation kinetics with exemplary substrates. All sequences were embedded in a constant TTGCACTCTCCNNNCGNNNGTCCCAGCTTC flanking sequence context outside of the ±3 flanking region and annealed with methylated complementary strand. Substrate preferences of DNMT1 in the deep enzymology experiments are indicated by the rank of the substrate in the NNCGNN profile, where 1 represents the highest preferences and 256 the lowest. Methylation rates are presented as averages and standard deviations of three independent experiments. Representative primary data are show in Supplementary Fig. 4a. The central CpG site is printed in bold letters and the N2 flanks are underlined.
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