ArticlePLoS computational biology2020
Epigenome-based splicing prediction using a recurrent neural network.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 38 citations in OpenAlex.
- Emerin loss of function inhibits MyoD-driven differentiation of human iPSCs into skeletal myotubes.bioRxiv : the preprint server for biology · 2026Article
- EpGAT: integrating epigenetics and 3D genome structure to predict alternative splicing and polyadenylation.Briefings in bioinformatics · 2026Article
- Repeat expansions inbioRxiv : the preprint server for biology · 2026Article
- RNA-binding proteins connect Exon usage to the chromatin.NAR genomics and bioinformatics · 2025Article
- Machine learning on multiple epigenetic features reveals H3K27Ac as a driver of gene expression prediction across patients with glioblastoma.PLoS computational biology · 2025Article
- DurableMolecular therapy. Nucleic acids · 2025Article
- Most human DNA replication initiation is dispersed throughout the genome with only a minority within previously identified initiation zones.Genome biology · 2025Article
- From Data to Cure: A Comprehensive Exploration of Multi-omics Data Analysis for Targeted Therapies.Molecular biotechnology · 2025Review
- The potential impact of RNA splicing abnormalities on immune regulation in endometrial cancer.Cell death & disease · 2025Review
- The role of chromatin state in intron retention: A case study in leveraging large scale deep learning models.PLoS computational biology · 2025Article
- PTBP1-mediated repression of neuron-specific CDC42 splicing constitutes a genomic alteration-independent, developmentally conserved vulnerability in IDH-wildtype glioblastoma.Functional & integrative genomics · 2024Article
- bsgenova: an accurate, robust, and fast genotype caller for bisulfite-sequencing data.BMC bioinformatics · 2024Article
- Exhaustive identification of genome-wide binding events of transcriptional regulators.Nucleic acids research · 2024Article
- Article
- A hybrid approach of ensemble learning and grey wolf optimizer for DNA splice junction prediction.PloS one · 2024Article
- Differential exon usage of developmental genes is associated with deregulated epigenetic marks.Scientific reports · 2023Article
- 3D Chromatin Architecture Re-Wiring at theBiology · 2023Article
- Advances in alternative splicing identification: deep learning and pantranscriptome.Frontiers in plant science · 2023Article
- GoPeaks: histone modification peak calling for CUT&Tag.Genome biology · 2022Article
- Genes Possessing the Most Frequent DNA DSBs Are Highly Associated with Development and Cancers, and Essentially Overlap with the rDNA-Contacting Genes.International journal of molecular sciences · 2022Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Alternative RNA splicing provides an important means to expand metazoan transcriptome diversity. Contrary to what was accepted previously, splicing is now thought to predominantly take place during transcription. Motivated by emerging data showing the physical proximity of the spliceosome to Pol II, we surveyed the effect of epigenetic context on co-transcriptional splicing. In particular, we observed that splicing factors were not necessarily enriched at exon junctions and that most epigenetic signatures had a distinctly asymmetric profile around known splice sites. Given this, we tried to build an interpretable model that mimics the physical layout of splicing regulation where the chromatin context progressively changes as the Pol II moves along the guide DNA. We used a recurrent-neural-network architecture to predict the inclusion of a spliced exon based on adjacent epigenetic signals, and we showed that distinct spatio-temporal features of these signals were key determinants of model outcome, in addition to the actual nucleotide sequence of the guide DNA strand. After the model had been trained and tested (with >80% precision-recall curve metric), we explored the derived weights of the latent factors, finding they highlight the importance of the asymmetric time-direction of chromatin context during transcription.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.