Fig. 2

The ALKBH3 gene promoter region. a The ALKBH3 gene promoter is transcriptionally active in variant human mammary epithelial cells (vHMEC) based on available data from the Roadmap Epigenetic Consortium (Roadmap Epigenomics Consortium, Nature 2015). Data for vHMEC are shown here for markers associated with active transcription (H3K4me3 and H3K36me3) together with repressive markers (H3K27me3, H3K9me3, H3K4me1 and 5-methylcytosine (DNA methyl)). Additionally, DNAse and RNA sequencing results from vHMEC cells are shown – reflecting chromatin accessibility and mRNA expression, respectively. b The ALKBH3 gene promoter region is shown with respect to the FANTOM5 transcription start site (TSS) as arrows p1 and p2 along with the 1st exon and the promoter-associated CpG island (UCSC defined). The CpG methylation assay for ALKBH3 was designed to include CpG sites proximal to the TSS and the regions selected is indicated by a black box (labelled R) covering three closely spaced CpG dinucleotides found -50, −53 and -58 bp upstream of the major TSS (p1 region in FANTOM5). Additionally, the region where statistically significant associations were revealed between CpG methylation and loss of expression for the ALKBH3 gene in tumors is marked out and labelled for expression as “Xprs” (see further information in Additional file 1)