A protocol for the simultaneous analysis of gene DNA methylation and mRNA expression levels in the rodent brain

Abstract

Gene expression levels are associated with DNA methylation patterns of gene promoter regions, although the absence of correlation between mRNA levels and promoter methylation state can also be often observed. To elucidate the functional significance of DNA methylation for gene transcriptional activity, the simultaneous analysis of RNA expression and DNA methylation levels should be performed. In this chapter we introduce a protocol for extracting total RNA and genomic DNA from the same tissue sample of small size, followed by transcript expression analysis and bisulfite PCR. The purifi ed RNA can then be used for expression microarray, transcriptome or small RNA analyses by next-generation sequencing (NGS), while the bisulfite PCR products can be analyzed using capillary sequencing, pyrosequencing, or NGS.