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. 2016 Nov 24;8(3):5629–5637. doi: 10.18632/oncotarget.13562

Figure 1. Optimizing the DNA methylation resolution according to a biological context.

Figure 1

The most widely used strategy for integrating DNA methylation with gene regulation is to average CpG methylation signal throughout wide loci. A. The study of the imprinting regions can be achieved by averaging DNA methylation signal of loci ranging from 1 kb to 10 kb. B. Interplay between gene expression and DNA methylation are usually drawn by studying the DNA methylation level within the 1 kb to 5kb region surrounding the TSS. C. However, DNA methylation is involved in many other mechanisms. Extending the DNA methylation resolution to a 100 bp around splicing sites enables the investigation of exon inclusion. D. On the other hand, a 20 bp resolution was established to be optimal for studying the interplay between DNA methylation and nucleosome positioning. E. Finally, DNA methylation plays a key role in the recruitment of transcription factor and it has been shown that methylation of a single cytosine can affect protein/DNA binding affinity.