Darren Soanes from the University of Exeter in the UK spoke at London Calling about “DNA modifications in specific nuclei populations purified from human brain tissue.” Soanes is in the Complex Epigenetics Group at Exeter. They study cytosine modifications 5mC and 5hmC. The group has completed studies on methylation patterns in brain samples. Soanes noted that Oxford Nanopore Technologies (ONT) is a great tool for genomics and epigenomics. The team has developed a protocol based on fluorescence-activated nuclei sorting (FANS) of cortical cell types. These cells are then used for various omic tests. To do this, they extract DNA, shear with Covaris, use the Ligation Sequencing Kit 114, and sequence on PromethION flow cells on a P2 Solo. The group uses ModKit and Dorado to identify modifications. Soanes shared PCA plots of 5mC and 5hmC profiles in neurons and oligodendrocytes. The distribution of methylation across samples seems to be bimodal: most sites are either unmethylated or methylated. In neurons, there is a mixture. The group wanted to compare different technologies: ONT, Illumina array, Twist, and Epigenetix (CGEX). The approaches produced similar distribution profiles. With ONT, the reads could be phased with WhatsHap. The protocol they developed leverages FANS to isolate cell-type specific nuclei from post-mortem brain tissue and quantify methylation levels in 28 million CpG sites! Future studies will evaluate the link between methylation and hydroxymethylation and gene expression. I did not know about FANS and learned about it and how different methylation detection.
