TitleInvestigation of Transposon DNA Methylation and Copy Number Variation in Plants Using Southern Hybridisation.
Publication TypeJournal Article
Year of Publication2022
AuthorsG VHari Sunda, Shivaprasad PV
JournalBio Protoc
Date Published2022 Jun 05

Plant genomes are pronouncedly enriched in repeat elements such as transposons. These repeats are epigenetically regulated by DNA methylation. Whole genome high-depth sequencing after bisulfite treatment remains an expensive and laborious method to reliably profile the DNA methylome, especially when considering large genomes such as in crops. Here, we present a simple reproducible Southern hybridisation-based assay to obtain incontrovertible methylation patterns from targeted regions in the rice genome. By employing minor but key modifications, we reliably detected transposon copy number variations over multiple generations. This method can be regarded as a gold standard for validation of epigenetic variations at target loci, and the consequent proliferation of transposons, or segregation in several plant replicates and genotypes. .

Alternate JournalBio Protoc
PubMed ID35799912
PubMed Central IDPMC9243515