Discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiome using nanopore sequencing
About Alan Tourancheau
Alan Tourancheau is currently a Postdoctoral Fellow at Icahn School of Medicine at Mount Sinai. He completed his undergraduate studies in Bioinformatics at University of Nantes, and earned his Ph.D. in Pharmaceuticals Sciences from Laval University, Quebec in 2016. In his thesis work, he uncovered novel splicing events in metabolic enzymes’ transcriptome with deep targeted RNA sequencing. After completing his Ph.D., he joined Dr. Gang Fang’s team to develop DNA modification detection methods using third generation sequencing.
By examining three types of DNA methylation (6mA, 5mC, and 4mC) in a large assortment of sequence contexts across multiple bacteria, we observed complex heterogeneity of nanopore sequencing signal at methylated sites. To capture this complexity and enable methylation discovery in prokaryotes, we developed a novel method that can identify specific type and modified position of bacterial DNA methylation. We applied it to individual bacteria and mouse gut microbiomes for de novo methylation discovery, methylation binning of metagenomic contigs, association of mobile genetic elements with their host genomes, and identification of misassembled metagenomic contigs.