Sung won Lim from Binomica Labs in the USA did a flash talk at the Nanopore Community Meeting in 2022 about “MinION outcome in amateur research: three genomes from 2018 to 2022.” They started using MinION for fun as a “weekend project.” They sequenced Deinococcus radiophilus GCF 020889623.1 and compared it to other genomes deposited in GenBank. I should mention won Lim is a warehouse worker and self-described amateur biologist. They used ONT Rapid Kits and explored different genome extraction kits… between 9 PM and 3 am! Along with a friend, they went further and compared replication protein A. They then collaborated with MacLea to assemble a Halococcus dombrowskii. With newfound confidence, in 2022 they sequenced the Oxalis stricta chloroplast. I am impressed with their journey and growth. In three years they went from optimizing DNA extractions to collaborating with labs and sequencing chloroplasts.
Next, Franziska Haarich from the University of Lubeck, Germany, presented “CRISPRoff as potential treatment strategy for collagen VI congenital muscular dystrophy,” also a short session. This work is part of Haarich’s doctoral project. They explained collage VI congenital muscular dystrophy (COL VI-CMD) and how it is caused by mutations in six collagen genes. The primary manifestations are hypermobility as well as contractions. The structure of a key tetramer is disrupted with a mutation. COL VI-CMD is rare, and Haarich is trying to find an approach that is mutation-independent. For this, they are using CRISPRoff, that is epigenome editing. They encountered some difficulties extracting high-molecular DNA, and they now use the NEB Monarch kit. I do too and have found it to be very useful! They now have wet-lab protocols and a bioinformatics pipeline. To address some transfection challenges, they transfect components to create virus-like particles with what is needed for CRISPRoff allele-specific methylation. While the methods are still being refined, this approach could be very powerful! I wonder if we can take advantage of CRISPRoff for phage genome editing…
