ArticleNucleic acids research2017
Fractionation iCLIP detects persistent SR protein binding to conserved, retained introns in chromatin, nucleoplasm and cytoplasm.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 66 citations in OpenAlex.
- Isotope-free mapping of protein-RNA interactions at single-nucleotide resolution by iCLIP3.STAR protocols · 2026Article
- Bclaf1 drives heart failure by recruiting Srsf2 to enhance Hand2 pre-mRNA splicing and pathological hypertrophy.Nature communications · 2026Article
- Regulation of oncogenic C-terminal truncated p53β protein isoform expression by SRSF3-UPF1 splicing and surveillance axis.Cell & bioscience · 2026Article
- Progress and challenges in profiling protein-RNA and protein-associated RNA-RNA interactions.RNA (New York, N.Y.) · 2026Review
- Interplay between RNA-protein interactions and RNA structures in gene regulation.FEBS open bio · 2026Review
- Multidimensional regulatory roles and therapeutic applications of SRSF7 in cancer.Cell death discovery · 2025Review
- RBProximity-CLIP Enables Subcellular Mapping of RNA-Binding Protein Interactions at Nucleotide Resolution.bioRxiv : the preprint server for biology · 2025Article
- snoCLASH Reveals Extensive snoRNA-mRNA Interaction Networks.bioRxiv : the preprint server for biology · 2025Article
- Argonautes and small RNAs associated with nematode programmed DNA elimination.bioRxiv : the preprint server for biology · 2025Article
- Long-read Sequencing of Nascent RNA from Budding and Fission Yeasts.bioRxiv : the preprint server for biology · 2025Article
- Antisense oligonucleotide-mediated TRA2β poison exon inclusion induces the expression of a lncRNA with anti-tumor effects.Nature communications · 2025Article
- Mapping RNA-protein interactions with subcellular resolution using colocalization CLIP.RNA (New York, N.Y.) · 2024Article
- Decryption of sequence, structure, and functional features of SINE repeat elements in SINEUP non-coding RNA-mediated post-transcriptional gene regulation.Nature communications · 2024Article
- ORC1 binds to cis-transcribed RNAs for efficient activation of replication origins.Nature communications · 2023Article
- A network of DZF proteins controls alternative splicing regulation and fidelity.Nucleic acids research · 2023Article
- Review
- PABPN1 prevents the nuclear export of an unspliced RNA with a constitutive transport element and controls human gene expression via intron retention.RNA (New York, N.Y.) · 2023Article
- SRSF7 and SRSF3 depend on RNA sequencing motifs and secondary structures to regulate Microprocessor.Life science alliance · 2023Article
- Oncogenic SRSF3 in health and diseases.International journal of biological sciences · 2023Review
- Deconvolution of in vivo protein-RNA contacts using fractionated eCLIP-seq.STAR protocols · 2022Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
RNA binding proteins (RBPs) regulate the lives of all RNAs from transcription, processing, and function to decay. How RNA-protein interactions change over time and space to support these roles is poorly understood. Towards this end, we sought to determine how two SR proteins-SRSF3 and SRSF7, regulators of pre-mRNA splicing, nuclear export and translation-interact with RNA in different cellular compartments. To do so, we developed Fractionation iCLIP (Fr-iCLIP), in which chromatin, nucleoplasmic and cytoplasmic fractions are prepared from UV-crosslinked cells and then subjected to iCLIP. As expected, SRSF3 and SRSF7 targets were detected in all fractions, with intron, snoRNA and lncRNA interactions enriched in the nucleus. Cytoplasmically-bound mRNAs reflected distinct functional groupings, suggesting coordinated translation regulation. Surprisingly, hundreds of cytoplasmic intron targets were detected. These cytoplasmic introns were found to be highly conserved and introduced premature termination codons into coding regions. However, many intron-retained mRNAs were not substrates for nonsense-mediated decay (NMD), even though they were detected in polysomes. These findings suggest that intron-retained mRNAs in the cytoplasm have previously uncharacterized functions and/or escape surveillance. Hence, Fr-iCLIP detects the cellular location of RNA-protein interactions and provides insight into co-transcriptional, post-transcriptional and cytoplasmic RBP functions for coding and non-coding RNAs.
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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.