Post-transcriptional splicing can occur in a slow-moving zone around the gene
Data files
Apr 05, 2024 version files 124.38 GB
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Cote_eLife_raw_data_1.zip
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Cote_eLife_raw_data_2.zip
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Cote_eLife_raw_data_3.zip
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Cote_eLife_raw_data_4.zip
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Cote_eLife_raw_data_5.zip
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Cote_eLife_raw_data_6.zip
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Cote_eLife_scripts.zip
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README.md
Abstract
Splicing is the stepwise molecular process by which introns are removed from pre-mRNA and exons are joined together to form mature mRNA sequences. The ordering and spatial distribution of these steps remains controversial, with opposing models suggesting splicing occurs either during or after transcription. We used single-molecule RNA FISH, expansion microscopy, and live-cell imaging to reveal the spatiotemporal distribution of nascent transcripts in mammalian cells. At super-resolution levels, we found that pre-mRNA formed clouds around the transcription site. These clouds indicate the existence of a transcription site proximal zone through which RNA moves more slowly than in the nucleoplasm. Full-length pre-mRNA undergoes continuous splicing as they move through this zone following transcription, suggesting a model in which splicing can occur post-transcriptionally but still within the proximity of the transcription site, thus seeming co-transcriptional by most assays. These results may unify conflicting reports of co-transcriptional versus post-transcriptional splicing.
README: Post-transcriptional splicing can occur in a slow-moving zone around the gene
https://doi.org/10.5061/dryad.m0cfxppb7
Description of the data and file structure
Matlab scripts in the extraction_scripts folder were used to generate data in the extracted_data and extracted_images folders. This data was analyzed by R and Matlab scripts in the analysis_scripts folder. Analyzed data was plotted into figure graphs using the R scripts in the plot_scripts folder.
Folder structure:
Cote_eLife_scripts
- /analysis_scripts: R and .m files
- /extracted_data: CSV files with information about genes, etc., and .tif images, STORM density maps
- /extracted_images: organized .tif files
- /extraction_scripts: .m scripts
- /plot_scripts: R scripts for plots
Cote_eLife_raw_data_1 - Cote_eLife_raw_data_6
These folders contain .tif images of cells, and some contain matlab files with the corresponding data.
Sharing/Access information
Sequencing data generated for this paper can be found on GEO under accession number GSE254859.
Code/Software
Image analysis requires the RajLabImageTools pipeline, found at the GitHub link in the Related Works section.