Secondary structural ensembles of the SARS-CoV-2 RNA genome in infected cells

Analyze quality of structural model, structural ensembles, and comparisons to models by Pyle, Incarnato, and Das labs.

files

• plots.xlsx: description of data used in generating the plots in the following figures:
  • Fig 4b
  • Fig 5b

directories

scripts

• run_analysis.py: performs most of the analyses and generates data and plots for the following figures:
  • Fig 1: b, c, d
  • Fig 2: a, b
  • Fig 3
  • Fig S2: b, c
  • Fig S3
  • Fig S4
  • Fig S5
  • Fig S6: a, b
  • Fig S7: b, c
  • Fig S10: a, b
• models.py: a module for loading structural information from our models, Manfredonia et al., Huston et al., and Sun et al.; imported by run_analysis
• compare_to_rangan.py: compares structure to model from Rangan et al. and generates the following figures:
  • Fig S8: a, b, c, d, e, f
  • Fig S9: a
• make_files_for_fig5_ldi.py: make the raw files used in preparing the structure models in Fig 5
• cm.py: perform covariation analysis on the structure of the SARS-CoV-2 genome; not used for any figures but appears in our responses to reviewers.
• get_db_seq_matching_ref_genome.py: find the sequence in the SARS-CoV-2 sequence database that matches the reference genome
• fold_genomes.py: fold the SARS-2 genome using staggered windows to remove edge effects; results were extremely similar to ignoring edge effects, so not used in this paper
• TRS_boundaries.py: Compute how many bases on each side of a TRS core sequence should be required for counting the TRS as unambiguously part of gRNA; not used for any results in this paper
• compare_to_zhang.py: Compare our results to the model from Zhang et al. (2021). Nat. Comm. 12: 5695; not used for any results in this paper
• ct2dot.py: convert an RNA structure in CT format to dot-bracket format

models

• controls: structure models of SARS-CoV-2 SL5, HIV RRE, and U4/U6 snRNA
• Huston: SHAPE reactivities and structure model from Huston et al.
• Manfredonia: SHAPE and DMS reactivities and structure model from Manfredonia et al.
• Sun: icSHAPE reactivities and structure model from Sun et al.
• Zhang: structure models of the SARS-CoV-2 FSE from Zhang et al.
• Lan: lists of files of structure models

fold

structure models of staggered regions of the SARS-CoV-2 based on the Vero and Huh7 DMS-MaPseq reactivities