ArticleAmerican journal of human genetics2019
Discovery of Allele-Specific Protein-RNA Interactions in Human Transcriptomes.
Article in American journal of human genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- DirectASRM: uncovering allele-specific post-transcriptional RNA modifications through direct RNA sequencing.Bioinformatics (Oxford, England) · 2026Article
- Augmented prediction of multi-species protein-RNA interactions using evolutionary conservation of RNA-binding proteins.Nature communications · 2026Article
- Genetic alternative splicing regulation mapping of cartilage and synovium reveals tissue-specific mechanisms of joint-related traits.Nature communications · 2026Article
- Sequence and parent-of-origin dependent mThe EMBO journal · 2025Article
- M6Allele: a toolkit for detection of allele-specific RNA N6-methyladenosine modifications.GigaScience · 2025Article
- AStruct: detection of allele-specific RNA secondary structure in structuromic probing data.BMC bioinformatics · 2024Article
- Nuclear and cytoplasmic specific RNA binding proteome enrichment and its changes upon ferroptosis induction.Nature communications · 2024Article
- Allele-specific RNAGenome research · 2023Article
- Inferring RNA-binding protein target preferences using adversarial domain adaptation.PLoS computational biology · 2022Article
- Diagnostic and therapeutic potential of RNASET2 in Crohn's disease: Disease-risk polymorphism modulates allelic-imbalance in expression and circulating protein levels and recombinant-RNASET2 attenuates pro-inflammatory cytokine secretion.Frontiers in immunology · 2022Article
- Predicting dynamic cellular protein-RNA interactions by deep learning using in vivo RNA structures.Cell research · 2021Article
- NCBP3/SNHG6 inhibits GBX2 transcription in a histone modification manner to facilitate the malignant biological behaviour of glioma cells.RNA biology · 2021Article
- Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins.Genome biology · 2020Article
- Prevalence and architecture of posttranscriptionally impaired synonymous mutations in 8,320 genomes across 22 cancer types.Nucleic acids research · 2020Article
- Deep neural networks for interpreting RNA-binding protein target preferences.Genome research · 2020Article
- Gain-of-Function Mutations: An Emerging Advantage for Cancer Biology.Trends in biochemical sciences · 2019Review
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Authors and funding
2 authors.
Funding
Abstract
Gene expression is tightly regulated at the post-transcriptional level through splicing, transport, translation, and decay. RNA-binding proteins (RBPs) play key roles in post-transcriptional gene regulation, and genetic variants that alter RBP-RNA interactions can affect gene products and functions. We developed a computational method ASPRIN (Allele-Specific Protein-RNA Interaction) that uses a joint analysis of CLIP-seq (cross-linking and immunoprecipitation followed by high-throughput sequencing) and RNA-seq data to identify genetic variants that alter RBP-RNA interactions by directly observing the allelic preference of RBP from CLIP-seq experiments as compared to RNA-seq. We used ASPRIN to systematically analyze CLIP-seq and RNA-seq data for 166 RBPs in two ENCODE (Encyclopedia of DNA Elements) cell lines. ASPRIN identified genetic variants that alter RBP-RNA interactions by modifying RBP binding motifs within RNA. Moreover, through an integrative ASPRIN analysis with population-scale RNA-seq data, we showed that ASPRIN can help reveal potential causal variants that affect alternative splicing via allele-specific protein-RNA interactions.
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