Figure 8.2.

MethylViewer plot of chromatin at the human NF1 promoter in NSCs. (A) The 303-bp amplicon was on the transcribed strand ~200 bp 5′ of the NF1 transcription start site (bent arrow) and gene body (dark blue bar), overlapping both a CG island (annotated by UCSC Genome Browser; http://genome.ucsc.edu/; Dreszer et al., 2012; Fujita et al., 2011), and sites hypersensitive to DNase I in several cell lines (Sabo et al., 2006). Nucleotide coordinates on chromosome 17 are indicated at the top. (B) MethylViewer plot (to scale with A) of 10 molecules randomly chosen from over 1000 sequenced with forward primer. Of these, four featured a protected footprint on the nucleosome scale, marked by the light blue shading. Note that the top two molecules appear to be duplicates, having identical unconverted HCH site and methylation status of all sites. Nucleosome core particle length is indicated by bar with light blue shading. (C) Plot of 10 randomly chosen from over 6000 sequenced with the reverse primer.