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A guide to computational cotranscriptional folding - Data and Scripts

This repository contains data, scripts and other resources for the DrTutorial book chapter

"A guide to computational cotranscriptional folding featuring the SRP RNA"

Below is a list of resources collected within this repository together with their references and sources (if applicable).

Installation

The resources can be installed globally via pip:

pip install .

or locally in the users home directory via:

pip install --user .

FASTA formatted RNA sequence files

The sequences/ directory contains the following FASTA-formatted sequences:

sequence id local file data set (sequence name) reference
SRPn SRPn.fa Native E.coli SRP sequence [1], [2], [3], [4]
SRPt SRPt.fa Trapped E.coli SRP mutant (U21C) [1], [3]
SRPr SRPr.fa Rescue E.coli SRP mutant (U21C/C22U/G93A) [1]
SRPf SRPf.fa Folding-path E.coli SRP mutant (U35C/U37C) [3]

and additional structural motifs of transient helices in FASTA format with dot-bracket structures as reported in literature and within this tutorial:

sequence id local file description reference
SRPn SRPn-H1.fa Transient helix H1 [1],[3]
SRPn SRPn-H1a.fa Transient helix H1a [4]
SRPn SRPn-H1b.fa Transient helix H1b [3]
SRPn SRPn-H1c.fa Transient helix H1c
SRPn SRPn-H1-H2-R1-H3.fa Transient helices H1, H2, R1, and H3 [1],[3]
SRPn SRPn-H1c-H2a-H3a.fa Transient helices H1c, H2a, and H3a [1]
SRPn SRPn-H2-R1-R2.fa Functional conformation with helices H2, R1, and R2 [1],[2],[3]

SHAPE reactivity data

The SHAPE/ directory contains co-transcriptional SHAPE data provided by [1] and [2] and downloaded from the RMDB database.

sequence id local file data set (with link to RMDB) reference
SRPn SRPECLI_BZCN_0001.rdat Replicate 1 for native E.coli SRP sequence [2]
SRPn SRPECLI_BZCN_0002.rdat Replicate 2 for native E.coli SRP sequence [2]
SRPn SRPECLI_BZCN_0003.rdat Replicate 3 for native E.coli SRP sequence [2]
SRPn SRPECLI_BZCN_0004.rdat Equilibrium refold for native E.coli SRP sequence [2]
SRPt SRPU21C_BZCN_0001.rdat Replicate 1 for trapped E.coli SRP mutant (U21C) [1]
SRPt SRPU21C_BZCN_0002.rdat Replicate 2 for trapped E.coli SRP mutant (U21C) [1]
SRPt SRPU21C_BZCN_0003.rdat Replicate 3 for trapped E.coli SRP mutant (U21C) [1]
SRPt SRPU21C_BZCN_0004.rdat Equilibrium refold 1 for trapped E.coli SRP mutant (U21C) [1]
SRPt SRPU21C_BZCN_0005.rdat Equilibrium refold 2 for trapped E.coli SRP mutant (U21C) [1]
SRPr SRP21CR_BZCN_0001.rdat Replicate 1 for rescue E.coli SRP mutant (U21C/C22U/G93A) [1]
SRPr SRP21CR_BZCN_0002.rdat Replicate 2 for rescue E.coli SRP mutant (U21C/C22U/G93A) [1]
SRPr SRP21CR_BZCN_0003.rdat Replicate 3 for rescue E.coli SRP mutant (U21C/C22U/G93A) [1]

Python and R scripts

The scripts/ directory contains various prediction-, parser- and plotting scripts.

script name purpose
thermo_predict.py Predict thermodynamic equilibrium profiles for energies and accessibilities of nascent transcripts
drf_parser.py Parser for *.drf output as produced by the DrTransformer and DrKinfold programs
convert_rdat.py Convert cotranscriptional SHAPE reactivity data from RMDBs .rdat files into the CSV format produced by drf_parser.py and thermo_predict.py
plot_energy_bands.R Produce an energy distribution plot for cotranscriptionally formed structures
plot_accessibility.R Plot accessibility profiles for nascent transcripts
make_SRP_images.sh Create annotated secondary structure plots of the transient helix motifs

Additionally, in the drconverters/ directory, this repository contains a snapshot of the drconverters script package. This package will be automagically included in the installation process.

References

  • [1] Yu, A. M., Gasper, P. M., Cheng, L., Lai, L. B., Kaur, S., Gopalan, V., Chen, A. A., and Lucks, J. B. (2021). "Computationally reconstructing cotranscriptional RNA folding from experimental data reveals rearrangement of non-native folding intermediates.", Molecular cell , 81(4), 870-883.
  • [2] Watters, K. E., Strobel, E. J., Yu, A. M., Lis, J. T., and Lucks, J. B. (2016). "Cotranscriptional folding of a riboswitch at nucleotide resolution.", Nature structural & molecular biology, 23(12), 1124.
  • [3] Fukuda, S., Yan, S., Komi, Y., Sun, M., Gabizon, R., and Bustamante, C. (2020). "The biogenesis of SRP RNA is modulated by an RNA folding intermediate attained during transcription.", Molecular Cell , 77(2), 241-250.
  • [4] Wong, T. N., Sosnick, T. R., and Pan, T. (2007). "Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures.", Proceedings of the National Academy of Sciences, 104(46), 17995-18000.

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