In the last decade there has been a tremendous growth in epigenetic research, demonstrated by the publication of more than 10,000 articles only in 2013. This expansion of the epigenetic area is mostly driven by cancer-related research and an associated search for suitable biomarkers. Despite an increasing interest in histone modifications and non-coding RNA, the majority of epigenetic studies still focus on DNA methylation using bisulfite treatment.
In this study we have looked at a classical approach for DNA methylation analysis as well as how potential improvements can be made to the procedure. Indeed, the standard experimental workflow contains 4 steps (DNA extraction, DNA conversion, DNA amplification and finally the analysis of the DNA) which can be resource consuming, as each individual step requires optimisation and so represents a technical challenge. A standard and an improved approach focusing mainly on the first 3 steps of the workflow were compared using the methylation status of the haemoglobin beta locus (HBB) as a model. DNA was obtained from human blood samples.
Our results show that the standard process can be shortened without compromising quality or performance. Similarly, we have demonstrated that the ease with which converted DNA can be amplified using Bioline’s latest EPIKTM Amplification kit. In addition, a comparative analysis of the sequences of the resulting PCR products with non-bisulfite treated DNA has allowed us to determine that the quality of the methylation analysis is not affected by the new protocols.
In conclusion, we showed in this work that methylation analysis using standard bisulfite conversion can be improved with a faster workflow and less optimization or troubleshooting.