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).
The resources can be installed globally via pip:
pip install .
or locally in the users home directory via:
pip install --user .
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] |
The SHAPE/ directory contains co-transcriptional SHAPE data provided by [1] and [2] and downloaded from
the RMDB database.
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.
- [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.