ArticleGenes & development2018
Coordinate regulation of alternative pre-mRNA splicing events by the human RNA chaperone proteins hnRNPA1 and DDX5.
Article in Genes & development, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- Tools for Experimental and Computational Genome-Wide Analysis of the Function of DDX5 and DDX17 Helicases in RNA Processing.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Spatial transcriptomics reveals coordinated ventricular patterning and maturation in the developing human heart.Nature communications · 2026Article
- Multi-omics atlas of ovarian cellular and molecular responses to diabetes.Molecular metabolism · 2026Article
- Oncogenic DEAD-box ATPase DDX41 establishes transcript ensembles via CLK3-dependent and -independent mechanisms.Nature communications · 2025Article
- Computational investigation of the sequence context of arginine/glycine-rich motifs in the human proteome.BMC genomics · 2025Article
- Post-transcriptional control of KRAS: functional roles of 5'UTR RNA G-quadruplexes, long noncoding RNA, and hnRNPA1.Nucleic acids research · 2025Article
- Alternative pre-mRNA Splicing and Gene Expression Patterns in Midbrain Lineage Cells Carrying Familial Parkinson's Disease Mutations.bioRxiv : the preprint server for biology · 2025Article
- Supinoxin blocks small cell lung cancer progression by inhibiting mitochondrial respiration through DDX5.iScience · 2025Article
- LTA4H improves the tumor microenvironment and prevents HCC progression via targeting the HNRNPA1/LTBP1/TGF-β axis.Cell reports. Medicine · 2025Article
- RNA splicing in bone diseases: mechanisms, pathogenesis and therapeutics.Acta biochimica Polonica · 2025Review
- Article
- Superenhancer-driven circRNA Myst4 involves in pulmonary artery smooth muscle cell ferroptosis in pulmonary hypertension.iScience · 2024Article
- Post-transcriptional regulation of DEAD-box RNA helicases in hematopoietic malignancies.Genes & diseases · 2024Review
- A mutation in the low-complexity domain of splicing factor hnRNPA1 linked to amyotrophic lateral sclerosis disrupts distinct neuronal RNA splicing networks.Genes & development · 2024Article
- hnRNP A1 dysfunction alters RNA splicing and drives neurodegeneration in multiple sclerosis (MS).Nature communications · 2024Article
- SplicingLore: a web resource for studying the regulation of cassette exons by human splicing factors.Database : the journal of biological databases and curation · 2023Article
- Modulatory role of RNA helicases in MBNL-dependent alternative splicing regulation.Cellular and molecular life sciences : CMLS · 2023Article
- Article
- RNA binding protein DDX5 restricts RORγtScience advances · 2023Article
- The RGG motif proteins: Interactions, functions, and regulations.Wiley interdisciplinary reviews. RNA · 2023Review
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Alternative premessenger RNA (pre-mRNA) splicing is a post-transcriptional mechanism for controlling gene expression. Splicing patterns are determined by both RNA-binding proteins and nuclear pre-mRNA structure. Here, we analyzed pre-mRNA splicing patterns, RNA-binding sites, and RNA structures near these binding sites coordinately controlled by two splicing factors: the heterogeneous nuclear ribonucleoprotein hnRNPA1 and the RNA helicase DDX5. We identified thousands of alternative pre-mRNA splicing events controlled by these factors by RNA sequencing (RNA-seq) following RNAi. Enhanced cross-linking and immunoprecipitation (eCLIP) on nuclear extracts was used to identify protein-RNA-binding sites for both proteins in the nuclear transcriptome. We found a significant overlap between hnRNPA1 and DDX5 splicing targets and that they share many closely linked binding sites as determined by eCLIP analysis. In vivo SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) chemical RNA structure probing data were used to model RNA structures near several exons controlled and bound by both proteins. Both sequence motifs and in vivo UV cross-linking sites for hnRNPA1 and DDX5 were used to map binding sites in their RNA targets, and often these sites flanked regions of higher chemical reactivity, suggesting an organized nature of nuclear pre-mRNPs. This work provides a first glimpse into the possible RNA structures surrounding pre-mRNA splicing factor-binding sites.
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