Usability of human Infinium MethylationEPIC BeadChip for mouse DNA methylation studies

• Main Authors: Maria Needhamsen, Ewoud Ewing, Harald Lund, David Gomez-Cabrero, Robert Adam Harris, Lara Kular, Maja Jagodic
• Format: Article
• Language: English
• Published: BMC 2017-11-01
• Series: BMC Bioinformatics
• Subjects: Epigenetics; DNA methylation; Infinium BeadChip; Epic; Mouse; Rat
• Online Access: http://link.springer.com/article/10.1186/s12859-017-1870-y

Abstract Background The advent of array-based genome-wide DNA methylation methods has enabled quantitative measurement of single CpG methylation status at relatively low cost and sample input. Whereas the use of Infinium Human Methylation BeadChips has shown great utility in clinical studies, no equivalent tool is available for rodent animal samples. We examined the feasibility of using the new Infinium MethylationEPIC BeadChip for studying DNA methylation in mouse. Results In silico, we identified 19,420 EPIC probes (referred as mEPIC probes), which align with a unique best alignment score to the bisulfite converted reference mouse genome mm10. Further annotation revealed that 85% of mEPIC probes overlapped with mm10.refSeq genes at different genomic features including promoters (TSS1500 and TSS200), 1st exons, 5′UTRs, 3′UTRs, CpG islands, shores, shelves, open seas and FANTOM5 enhancers. Hybridization of mouse samples to Infinium Human MethylationEPIC BeadChips showed successful measurement of mEPIC probes and reproducibility between inter-array biological replicates. Finally, we demonstrated the utility of mEPIC probes for data exploration such as hierarchical clustering. Conclusions Given the absence of cost and labor convenient genome-wide technologies in the murine system, our findings show that the Infinium MethylationEPIC BeadChip platform is suitable for investigation of the mouse methylome. Furthermore, we provide the “mEPICmanifest” with genomic features, available to users of Infinium Human MethylationEPIC arrays for mouse samples.