ArticleRNA (New York, N.Y.)2019
RBP-Maps enables robust generation of splicing regulatory maps.
Article in RNA (New York, N.Y.), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
- A novel NLP-based method and algorithm to discover RNA-binding protein (RBP) motifs, contexts, binding preferences, and interactions.RNA (New York, N.Y.) · 2026Article
- Integrative CRISPR Screening and RNA Analyses Discover an Essential Role for PUF60 Interactions with 3' Splice Sites in Cancer Progression.Cancer research · 2026Article
- CCDC137: A key hub for RNA and epigenetic regulation in cancer research (Review).International journal of oncology · 2026Review
- QKI ensures splicing fidelity during cardiogenesis by engaging the U6 tri-snRNP to activate splicing at weak 5' splice sites.bioRxiv : the preprint server for biology · 2025Article
- Co-profiling of in situ RNA-protein interactions and transcriptome in single cells and tissues.Nature methods · 2025Article
- HIV-2 evades restriction by ZAP through adaptations in the U3 LTR region despite increased CpG levels.Nucleic acids research · 2025Article
- Hepatitis C virus NS3 helicase contributes to (-) strand RNA synthesis.Nature communications · 2025Article
- Computational Splicing Analysis of Transcriptomic Data Reveals Sulforaphane Modulation of Alternative mRNA Splicing of DNA Repair Genes in Differentiated SH-SY5Y Neurons.International journal of molecular sciences · 2025Article
- The dual role of RNA-binding proteins: promotion of tumorigenesis, drug resistance, and emerging therapeutic targets.Acta biochimica et biophysica Sinica · 2025Article
- CR-deal: Explainable Neural Network for circRNA-RBP Binding Site Recognition and Interpretation.Interdisciplinary sciences, computational life sciences · 2025Article
- The Rbfox1/LASR complex controls alternative pre-mRNA splicing by recognition of multipart RNA regulatory modules.Genes & development · 2025Article
- PDGFRα signaling regulates Srsf3 transcript binding to affect PI3K signaling and endosomal trafficking.eLife · 2024Article
- Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation.Molecular cell · 2024Article
- PDGFRα signaling regulates Srsf3 transcript binding to affect PI3K signaling and endosomal trafficking.bioRxiv : the preprint server for biology · 2024Article
- Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation.Molecular systems biology · 2024Article
- Development and validation of AI/ML derived splice-switching oligonucleotides.Molecular systems biology · 2024Article
- A phage nucleus-associated RNA-binding protein is required for jumbo phage infection.Nucleic acids research · 2024Article
- SHIFTR enables the unbiased identification of proteins bound to specific RNA regions in live cells.Nucleic acids research · 2024Article
- Bulk and single-cell alternative splicing analyses reveal roles of TRA2B in myogenic differentiation.Cell proliferation · 2024Article
- Profiling of RNA-binding protein binding sites by in situ reverse transcription-based sequencing.Nature methods · 2024Article
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5 authors.
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Abstract
Alternative splicing of pre-messenger RNA transcripts enables the generation of multiple protein isoforms from the same gene locus, providing a major source of protein diversity in mammalian genomes. RNA binding proteins (RBPs) bind to RNA to control splice site choice and define which exons are included in the resulting mature RNA transcript. However, depending on where the RBPs bind relative to splice sites, they can activate or repress splice site usage. To explore this position-specific regulation, in vivo binding sites identified by methods such as cross-linking and immunoprecipitation (CLIP) are integrated with alternative splicing events identified by RNA-seq or microarray. Merging these data sets enables the generation of a "splicing map," where CLIP signal relative to a merged meta-exon provides a simple summary of the position-specific effect of binding on splicing regulation. Here, we provide RBP-Maps, a software tool to simplify generation of these maps and enable researchers to rapidly query regulatory patterns of an RBP of interest. Further, we discuss various alternative approaches to generate such splicing maps, focusing on how decisions in construction (such as the use of peak versus read density, or whole-reads versus only single-nucleotide candidate crosslink positions) can affect the interpretation of these maps using example eCLIP data from the 150 RBPs profiled by the ENCODE consortium.
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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.