PT - JOURNAL ARTICLE AU - Zhen Wang AU - Jérôme Maluenda AU - Laurène Giraut AU - Thibault Vieille AU - Andréas Lefevre AU - David Salthouse AU - Gaël Radou AU - Rémi Moulinas AU - Sandra Astete-Morales AU - Pol d’Avezac AU - Geoff Smith AU - Charles André AU - Jean-François Allemand AU - David Bensimon AU - Vincent Croquette AU - Jimmy Ouellet AU - Gordon Hamilton TI - Detecting genetic variation and base modifications together in the same single molecules of DNA and RNA at base pair resolution using a magnetic tweezer platform AID - 10.1101/2020.04.03.002501 DP - 2020 Jan 01 TA - bioRxiv PG - 2020.04.03.002501 4099 - http://biorxiv.org/content/early/2020/04/04/2020.04.03.002501.short 4100 - http://biorxiv.org/content/early/2020/04/04/2020.04.03.002501.full AB - Accurate decoding of nucleic acid variation is important to understand the complexity and regulation of genome function. Here we introduce a single-molecule platform based on magnetic tweezer (MT) technology that can identify and map the positions of sequence variation and multiple base modifications together in the same single molecules of DNA or RNA at single base resolution. Using synthetic templates, we demonstrate that our method can distinguish the most common epigenetic marks on DNA and RNA with high sensitivity, specificity and precision. We also developed a highly specific CRISPR-Cas enrichment strategy to target genomic regions in native DNA without amplification. We then used this method to enrich native DNA from E. coli and characterized the differential levels of adenine and cytosine base modifications together in molecules of up to 5 kb in length. Finally, we enriched the 5‘UTR of FMR1 from cells derived from a Fragile X carrier and precisely measured the repeat expansion length and methylation status of each molecule. These results demonstrate that our platform can detect a variety of genetic, epigenetic and base modification changes concomitantly within the same single molecules.