Figure 1

Ultrastable cytosine guanine dinucleotides (CpGs) highlight a novel class of CpG islands (CGI). ( A ) Counts of 450 K samples disease tissue and germ layer samples used in analysis. [See Additional file 1: Table S2 for complete list of tissue types used]. ( B ) Representative CpGs of the methylation stability states (not ultrastable, ultrastable unmethylated and ultrastable methylated). Points represent an individual sample. Color scheme for ultrastable CpGs is maintained throughout the paper ( C ) Ultrastable CpGs allow observation of a unique resort methylation pattern. Composite profiles are shown for all 27,176 resorts on the 450 K. As CGIs have variable lengths, the CpG position within a CGI is shown here as relative to the length of the CGI. CGIs are plotted as 935.23 bp (mean length of all CGIs measured on the 450 K). Beyond the CGI boundaries on the plot (that is, start at 0 and end at 935.23), the CpGs actual distance, in base pairs, from the CGI start or end are used. Horizontal lines indicate the CGI, shore and shelf boundaries. The four panels show resorts with both types of ultrastable CpGs, only ultrastable unmethylated CpGs, only ultrastable methylated CpGs and no ultrastable CpGs. ( D ) Example resorts associated with the genes MARS (top; CGI chr12:57881750 to 57882035; ravine) and TBX5 (bottom; CGI chr12: 114845861 to 114847650; not ravine) are depicted with individual sample methylation patterns as smoothed lines showing the methylation pattern of an individual across the resort. Resort feature positions are indicated by colored labelled bars. Lines indicate positions of 450 K probes assaying the resorts, ultrastable CpGs are highlighted with taller red lines. The histogram shows CpG density for bins of 50 bp on a scale of 0 to 0.2 CpG/bp. The gene track is extracted from UCSC Genome browser hg19 (refseq track).