An illustrative example. Transcriptomic and epigenetic marks surrounding a gene (GIGFY1) that is expressed despite a hypermethylated promoter in esophagus tissue. As shown, the proximal promoter is highly methylated (red corresponds to high methylation, whereas green corresponds to low), and yet there is a large signal for gene expression, as can be seen in the RNA-seq signal track. An upstream CGI (in pink) >6 kb away is free of methylation, and transcription of the gene ensues at this locus extending into the body of the gene. These patterns suggest that (1) the longest transcript starts at the CGI as opposed to its annotated start site in Ensembl/GENCODE, (2) the first intron spans the segment region and extends into the body of the gene (in cyan), and (3) there is a large splice junction (loop in dark red) that is split between a region located inside the segment and an exon inside the annotated gene.
