ArticleNucleic acids research2019
Splicing of long non-coding RNAs primarily depends on polypyrimidine tract and 5' splice-site sequences due to weak interactions with SR proteins.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed, 75 citations in OpenAlex.
- Exon junction complex and nuclear pore complex components preferentially govern the nuclear export of spliced lncRNAs.Cell death discovery · 2026Article
- SpliceSelectNet: a hierarchical Transformer-based deep learning model for splice site prediction.Nucleic acids research · 2026Article
- Intron Retention Controls Localization of lncRNAsbioRxiv : the preprint server for biology · 2026Article
- Multidimensional regulatory roles and therapeutic applications of SRSF7 in cancer.Cell death discovery · 2025Review
- Splice site diversity and abundance of noncanonical introns in diplonemids (Diplonemea, Euglenozoa).RNA (New York, N.Y.) · 2025Article
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- Long Noncoding RNAs as Emerging Regulators of Seed Development, Germination, and Senescence.International journal of molecular sciences · 2025Review
- Dynamic interaction of spliceosomal snRNPs with coilin explains Cajal body characteristics.The Journal of cell biology · 2025Article
- Macrophage-derived lncRNAs in cancer: regulators of tumor progression and therapeutic targets.Medical oncology (Northwood, London, England) · 2025Review
- Retinitis pigmentosa-linked mutations impair the snRNA unwinding activity of SNRNP200 and reduce pre-mRNA binding of PRPF8.Cellular and molecular life sciences : CMLS · 2025Article
- Tumor-promoting effect and tumor immunity of SRSFs.Frontiers in cell and developmental biology · 2025Review
- Noncanonical formation of SNX5 gene-derived circular RNA regulates cancer growth.Cell death & disease · 2024Article
- CCAT1 lncRNA is chromatin-retained and post-transcriptionally spliced.Histochemistry and cell biology · 2024Article
- CaTCH: Calculating transcript complexity of human genes.MethodsX · 2024Article
- Cisplatin-induced PANDAR-Chemo-EVs contribute to a more aggressive and chemoresistant ovarian cancer phenotype through the SRSF9-SIRT4/SIRT6 axis.Journal of gynecologic oncology · 2024Article
- Article
- Genome-wide differential expression profiling of long non-coding RNAs in FOXA2 knockout iPSC-derived pancreatic cells.Cell communication and signaling : CCS · 2023Article
- Towards understandings of serine/arginine-rich splicing factors.Acta pharmaceutica Sinica. B · 2023Review
- Retinitis pigmentosa-associated mutations in mouse Prpf8 cause misexpression of circRNAs and degeneration of cerebellar granule cells.Life science alliance · 2023Article
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 3 countries.
Funding
Abstract
Many nascent long non-coding RNAs (lncRNAs) undergo the same maturation steps as pre-mRNAs of protein-coding genes (PCGs), but they are often poorly spliced. To identify the underlying mechanisms for this phenomenon, we searched for putative splicing inhibitory sequences using the ncRNA-a2 as a model. Genome-wide analyses of intergenic lncRNAs (lincRNAs) revealed that lincRNA splicing efficiency positively correlates with 5'ss strength while no such correlation was identified for PCGs. In addition, efficiently spliced lincRNAs have higher thymidine content in the polypyrimidine tract (PPT) compared to efficiently spliced PCGs. Using model lincRNAs, we provide experimental evidence that strengthening the 5'ss and increasing the T content in PPT significantly enhances lincRNA splicing. We further showed that lincRNA exons contain less putative binding sites for SR proteins. To map binding of SR proteins to lincRNAs, we performed iCLIP with SRSF2, SRSF5 and SRSF6 and analyzed eCLIP data for SRSF1, SRSF7 and SRSF9. All examined SR proteins bind lincRNA exons to a much lower extent than expression-matched PCGs. We propose that lincRNAs lack the cooperative interaction network that enhances splicing, which renders their splicing outcome more dependent on the optimality of splice sites.
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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.