Elena Bolshakova from Herzen State Pedagogical University of Russia presented at the Nanopore Community Meeting 2021 on “DNA methylation analysis of a tandem repeat specific to Coturnix japonica using nanopore sequencing.” They mentioned that tandem repeats are poorly understood and yet important for the regulation of gene expression and chromosomal structure. Nanopore sequencing allows methylation analyses and more information can be gleaned from studying repetitive sequences. Bolshakova studied Japanese quail (Coturnix japonica) with a genome that is 25% repetitive sequences! The CjapSAT repeat is specific to Japanese quail. Fish studies localized the tandem repeat and its effect on chromosome structure. Bolshakova prepared DNA from blood cells and 226-hour embryos. DNA extraction was performed with the NEB Monarch DNA Extraction kit and precipitated with ethanol before sequencing on a MinION Mk1B using R9.4.1 flow cells and the ligation sequencing kit SQK-LSK109. Data analysis was performed with Megalodon with basecalling with Guppy, Rerio, minimap2 mapping, and methylation calling. This workflow produced BAM and BED files. Samtools were used to analyze the BAM files and sort them. Bolshakova concluded that CjapSAT was methylated in the samples studies and some of the methylated repeat regions were differentially methylated. I had not considered using methylation analysis and Nanopore sequencing to learn about the tandem repeats and their features.
