NCM 2021: DNA methylation analysis of a tandem repeat specific to Coturnix japonica using nanopore sequencing

Nanopore sequencing was used to study differences in the methylation status of individual DNA monomers in Japanese quail (Coturnix japonica). Approximately 25% of the quail genome is methylated. Tandem repeats in genomes remain poorly understood but many are methylated and are thought to regulate gene expression and play a role in the structural organisation of chromosomes. The Cjap-STAT (MH475922) repeat is pericentromeric and is specific to Japanese quail. This repeat was studied for its methylation pattern. Two libraries were prepared using early embryos (36 h) and blood cells, and analysed using the MinION, producing FAST5 format raw reads. The highest accuracy was achieved using Megalodon with the basecalling model in Rerio. BAM and BED alignment files were created for analysis. Elena was 'expecting to find large numbers of methylated monomers in the repeats'; however, many unmethylated monomers were seen. In addition, many of the DNA monomers that were methylated in blood cells were unmethylated in the early embryo, suggesting methylation occurs later in development.