Computational epigenetic profiling of CpG islets in MTHFR Keat Wei • Heidi Sutherland • Emily Camilleri • Larisa M. Haupt • Lyn R. Griffiths • Siew Hua Gan Received: 30 September 2013 / Accepted: 3 September 2014 Ó Springer Science+Business Media Dordrecht 2014 Abstract Computational epigenetics is a new area of research focused on exploring how DNA methylation patterns affect transcription factor binding that affect gene expression patterns. The aim of this study was to produce a new protocol for the detection of DNA methylation patterns using computational analysis which can be fur- ther confirmed by bisulfite PCR with serial pyrose- quencing. The upstream regulatory element and pre- initiation complex relative to CpG islets within the methylenetetrahydrofolate reductase gene were deter- mined via computational analysis and online databases. The 1,104 bp long CpG island located near to or at the alternative promoter site of methylenetetrahydrofolate reductase gene was identified. The CpG plot indicated that CpG islets A and B, within the island, contained 62 and 75 % GC content CpG ratios of 0.70 and 0.80–0.95, respectively. Further exploration of the CpG islets A and B indicates that the transcription start sites were GGC which were absent from the TATA boxes. In addition, although six PROSITE motifs were identified in CpG B, no motifs were detected in CpG A. A number of cis- regulatory elements were found in different regions within the CpGs A and B. Transcription factors were predicted to bind to CpGs A and B with varying affinities depending on the DNA methylation status. In addition, transcription factor binding may influence the expression patterns of the methylenetetrahydrofolate reductase gene by recruiting chromatin condensation inducing factors. These results have significant implications for the understanding of the architecture of transcription factor binding at CpG islets as well as DNA methylation pat- terns that affect chromatin structure. Keywords MTHFR Á Epigenetics Á Computational Á CpG Á Transcription factor Abbreviations TSS Transcription start site MBD Methyl-CpG binding domain proteins MTHFR Methylenetetrahydrofolate reductase DBTSS Database of transcription start sites ENCODE Encyclopedia of DNA elements ChIP-seq Chromatin immunoprecipitation-sequencing MRE Methyl-sensitive restriction enzyme MeDIP-seq DNA immunoprecipitation-sequencing H3K4me3 H3 lysine 4 trimethylation Introduction CpG islands have an exceptionally high frequency of CG dinucleotides that are distributed mainly at regulatory regions and the first exon of genes or are distributed in intergenic and repetitive Alu elements [1, 2]. In fact, 70 to Electronic supplementary material The online version of this article (doi:10.1007/s11033-014-3729-x) contains supplementary material, which is available to authorized users. K. Wei (&) Á S. H. Gan Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia e-mail: wynnelkw@gmail.com K. Wei Á H. Sutherland Á E. Camilleri Á L. M. Haupt Á L. R. Griffiths Institute of Health and Biomedical Innovation, Queensland University of Technology, Musk Ave, Kelvin Grove, QLD 4059, Australia e-mail: lyn.griffiths@qut.edu.au 123 Mol Biol Rep DOI 10.1007/s11033-014-3729-x