https://github.com/soedinglab/degradation_scripts

data analysis scripts for degradation pathway story
https://github.com/soedinglab/degradation_scripts

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data analysis scripts for degradation pathway story

• Host: GitHub
• URL: https://github.com/soedinglab/degradation_scripts
• Owner: soedinglab
• License: gpl-3.0
• Created: 2017-12-12T16:24:20.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2019-06-12T11:56:11.000Z (almost 7 years ago)
• Last Synced: 2025-01-09T06:51:25.858Z (over 1 year ago)
• Language: Jupyter Notebook
• Size: 4.41 MB
• Stars: 0
• Watchers: 6
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          

# Scripts for analysing PAR-CLIP data of RNA degradation factors in yeast

[Sohrabi-Jahromi, Salma, et al. "Transcriptome maps of general eukaryotic RNA degradation factors." eLife 8 (2019): e47040.](https://elifesciences.org/articles/47040)

### Summary:

RNA degradation pathways enable RNA processing, the regulation of RNA levels, and the surveillance of aberrant or poorly functional RNAs in cells. Here we provide transcriptome-wide RNA-binding profiles of 30 general RNA degradation factors in the yeast Saccharomyces cerevisiae. The profiles reveal the distribution of degradation factors between different RNA classes. They are consistent with the canonical degradation pathway for closed-loop forming mRNAs after deadenylation. Modeling based on mRNA half-lives suggests that most degradation factors bind intact mRNAs, whereas decapping factors are recruited only for mRNA degradation, consistent with decapping being a rate-limiting step. Decapping factors preferentially bind mRNAs with non-optimal codons, consistent with rapid degradation of inefficiently translated mRNAs. Global analysis suggests that the nuclear surveillance machinery, including the complexes Nrd1/Nab3 and TRAMP4, targets aberrant nuclear RNAs and processes snoRNAs.

![summary](summary.jpg)

### A guide on the scripts and notebooks based on the figures in our paper:

[Mockinbird](https://github.com/soedinglab/mockinbird) config files:

    preprocess.yaml

    postprocess.yaml

**Figure 1—figure supplement 1.** Biological replicate PAR-CLIP experiments have

high correlation.

    replicate_similarity.ipynb

**Figure 2.** Distribution of degradation factor cross-link sites over the yeast

transcriptome.

    enrichment_normalized.ipynb

**Figure 2—figure supplement 1.** Different transcript classes have comparable U-

content.

    U_content_check.ipynb

**Figure 2—figure supplement 2.** Metagene profiles for subunits of the TRAMP

complexes on snoRNA genes.

    metagene_density_graph.ipynb

**Figure 3.** Metagene analysis of degradation factor binding on mRNAs.

    heatmap_metageneplots.ipynb

**Figure 3—figure supplement 1.** Metagene profiles of yeast RNA degradation factors

centered on translation start and stop sites in comparison to TIF-annotated TSS

and pA sites.

    heatmap_metageneplots.ipynb

    

**Figure 4.** Surveillance of aberrant nuclear antisense RNAs by the exosome and the

TRAMP4 complex.

    heatmap_metageneplots.ipynb

**Figure 4—figure supplement 1.** Motif enrichment analysis shows enrichment of

Nrd1/Nab3 motifs for the TRAMP4 and the exosome complex.

    kmer_counting.ipynb

    

**Figure 5.** Global co-occupancy and co-localization analysis reveals unexpected

cooperation between factors from different complexes and pathways.

    co_occupancy.py

    co_localization.py

    co_occupancy.ipynb

    co_localization.ipynb

**Figure 5—figure supplement 1.** Co-occupancy for 74 RNA processing factors.

    co_occupancy.py

    co_occupancy.ipynb

**Figure 5—figure supplement 2.** Co-localization coefficients for all 74 RNA

processing factors.

**Figure 5—figure supplement 3.** Two-dimensional embedding of co-localization

between 74 RNA processing factors.

    co_localization.py

    co_localization.ipynb

    

**Figure 6.** Binding preferences reveal a link between decapping-mediated

degradation and translation.

    occupancy_by_features.ipynb

    codon_freq_bar.ipynb

    linear_regression.R

**Figure 6—figure supplement 1-9.**

    occupancy_by_features.ipynb

**Figure 7.** Location and recruitment of the decapping complex Dcp1/Dcp2 and

decapping enhancers Edc3, Dhh1, and Edc2.

    metagene_by_halflife.ipynb

    occupancy_by_features.ipynb

    kmer_counting.ipynb