RT Journal Article
SR Electronic
T1 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
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.04.03.002501
DO 10.1101/2020.04.03.002501
A1 Zhen Wang
A1 Jérôme Maluenda
A1 Laurène Giraut
A1 Thibault Vieille
A1 Andréas Lefevre
A1 David Salthouse
A1 Gaël Radou
A1 Rémi Moulinas
A1 Sandra Astete-Morales
A1 Pol d’Avezac
A1 Geoff Smith
A1 Charles André
A1 Jean-François Allemand
A1 David Bensimon
A1 Vincent Croquette
A1 Jimmy Ouellet
A1 Gordon Hamilton
YR 2020
UL http://biorxiv.org/content/early/2020/04/04/2020.04.03.002501.abstract
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.