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 - Archive ouverte HAL Accéder directement au contenu
Pré-Publication, Document De Travail Année : 2021

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

Zhen Wang
  • Fonction : Auteur
  • PersonId : 766969
  • IdRef : 192906518
Jérôme Maluenda
  • Fonction : Auteur
Laurène Giraut
  • Fonction : Auteur
Thibault Vieille
  • Fonction : Auteur
Andréas Lefevre
  • Fonction : Auteur
David Salthouse
  • Fonction : Auteur
Gaël Radou
  • Fonction : Auteur
Rémi Moulinas
  • Fonction : Auteur
Sandra Astete-Morales
Pol D’avezac
  • Fonction : Auteur
Geoff Smith
  • Fonction : Auteur
Charles André
  • Fonction : Auteur
Jean-François Allemand
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  • PersonId : 839439
David Bensimon
  • Fonction : Auteur
Jimmy Ouellet
  • Fonction : Auteur
Gordon Hamilton
  • Fonction : Auteur

Résumé

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.

Dates et versions

hal-03101029 , version 1 (06-01-2021)

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Zhen Wang, Jérôme Maluenda, Laurène Giraut, Thibault Vieille, Andréas Lefevre, et al.. 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. 2021. ⟨hal-03101029⟩
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