Analysis of DNA Methylation Profile in Plants by Chop-PCR

Plants, when challenged with any unfavorable condition, such as biotic or abiotic stress, adapt to the stress via physiological or structural changes. DNA methylation, an important epigenetic factor, plays an integral role in determining chromatin dynamicity and in turn regulates the process of gene transcription in eukaryotes. DNA methylation resulting in 5-methylcytosine interferes with the transcription process by hindering accessibility of the transcriptional machinery. Transcriptionally active genes are predominantly hypomethylated, whereas repressed genes exhibit hypermethylation. It can thus be interpreted that the presence of methylation in the promoter and upstream regions of loci represses their transcription and vice versa. Chop-PCR is a targeted DNA methylation detection technique that uses partial digestion by methylation-sensitive restriction enzymes (MSREs) followed by PCR amplification. The presence of cytosine methylation at the cleavage sites of the MSREs protects the DNA against digestion and therefore can be amplified using PCR. Enzymatic cleavage occurs unhindered at unmethylated restriction sites and subsequent PCR amplification of the target sequence is not observed.