morrislab/rna-lifecycle-ietswaart

RNA Lifecycle Prediction

Overview

An mRNA molecule’s path from transcription to translation involves traversing multiple cellular compartments. This dataset, processed by mRNABench from experimental data by Ietswaart et al. (2024), provides an isoform-resolved map of this process using direct RNA sequencing.

The underlying assay captures RNA flow dynamics by measuring the rates at which transcripts are released from chromatin, exported from the nucleus, and loaded onto polysomes for translation. While a transcript passes through all of these locations, its steady-state level leads to enrichment in a primary compartment.

Prediction Task

The task is a multi-label classification problem: predict the subcellular compartment(s) where a given mRNA transcript is depleted. Because mRNA can be present in multiple compartments simultaneously, a transcript can have more than one label.

Data Format

The dataset is structured with the following columns:

• target: A multi-hot binary vector indicating the subcellular compartment(s) of depletion. The label positions correspond to: [Chromatin, Cytoplasm, Polysome].

  • Labeling Method: A transcript is labeled '1' for a given compartment if its measured rate of flow (e.g., rate of release from chromatin) falls within the bottom 20th percentile of the distribution for all transcripts.

• cds: A binary track that marks the position of the first nucleotide in each codon within the coding sequence (CDS).

• splice: A binary track that marks the position of the 3' end of each exon, indicating splice sites.

Data Source and Attribution

This dataset was generated using raw data from Ietswaart et al. (2024), which was collected from the NCBI Gene Expression Omnibus (GEO).

When using this dataset, please cite the original work:

• Original Paper: Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle.
• Original Dataset Source: NCBI BioProject PRJNA858812
• Citation:

  Ietswaart R et al., "Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle.", Mol Cell, 2024 Jul 25;84(14):2765-2784.e16
  

This dataset is redistributed as part of the mRNABench suite: https://github.com/morrislab/mRNABench