Genome-scale deconvolution of RNA structure ensembles

Edoardo Morandi, Ilaria Manfredonia, Lisa M. Simon, Francesca Anselmi, Martijn J. van Hemert, Salvatore Oliviero and Danny Incarnato


SARS-CoV-2


RNA structure heterogeneity represents the major challenge when querying RNA structures with chemical probing. We here introduce DRACO, an algorithm for the deconvolution of coexisting RNA conformations from mutational profiling experiments. Analysis of the SARS-CoV-2 genome by DMS-MaPseq and DRACO identifies multiple regions folding into two mutually-exclusive conformations, including a conserved structural switch in the 3′ UTR. Our work opens the way to dissecting the heterogeneity of the RNA structurome.

File types:

RC: RNA Count (per base mutation count and coverage)
MM: Mutation Map (map of mutations per read, input for DRACO)
JSON: DRACO′s raw output
XML: Normalized reactivities
CM: Covariance model
Stockholm: Alignment of structurally-related CoVs

  cspA 5′ UTR (RC, MM, JSON and XML files) Download
  V. vulnificus add riboswitch (RC, MM, JSON and XML files) Download
  SARS-CoV-2 (RC, JSON and XML files) Download
  SARS-CoV-2 3'-UTR conformations (CM and Stockholm files) Download
  SARS-CoV-2, replicate #1 (MM file) Download
  SARS-CoV-2, replicate #2 (MM file) Download
  DRACO algorithm (source code)    GitHub