ArticleThe EMBO journal2021
High-resolution mapping of function and protein binding in an RNA nuclear enrichment sequence.
Article in The EMBO journal, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Decoding RNA-protein interactions using high-throughput methods.RNA biology · 2026Review
- RNA-Lexis: a probabilistic algorithm using a non-parametric segmentation logic to detect meaningful sequences in RNA.Nucleic acids research · 2026Article
- RNA-binding protein hnRNPK: a multifunctional regulator of skeletal muscle biology and disease.Biochemical Society transactions · 2026Review
- Nuclear import of malaria RNA rewires splicing in host immune cells.Cell reports · 2026Article
- Systematic analysis of the target recognition and repression by the Pumilio proteins.Nucleic acids research · 2024Article
- Massively parallel dissection of RNA in RNA-protein interactions in vivo.Nucleic acids research · 2024Article
- What has single-cell transcriptomics taught us about long non-coding RNAs in the ventricular-subventricular zone?Stem cell reports · 2023Article
- ZFC3H1 and U1-70K promote the nuclear retention of mRNAs with 5' splice site motifs within nuclear speckles.RNA (New York, N.Y.) · 2022Article
- Context-specific effects of sequence elements on subcellular localization of linear and circular RNAs.Nature communications · 2022Article
- Bioinformatics Approaches for Determining the Functional Impact of Repetitive Elements on Non-coding RNAs.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Nuclear import receptors and hnRNPK mediates nuclear import and stress granule localization of SIRLOIN.Cellular and molecular life sciences : CMLS · 2021Article
- High-resolution mapping of function and protein binding in an RNA nuclear enrichment sequence.The EMBO journal · 2021Article
- Exploring the Role of MicroRNAs and Associated Proteins in Multiple Sclerosis.Basic and clinical neuroscienceArticle
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The functions of long RNAs, including mRNAs and long noncoding RNAs (lncRNAs), critically depend on their subcellular localization. The identity of the sequences that dictate subcellular localization and their high-resolution anatomy remain largely unknown. We used a suite of massively parallel RNA assays and libraries containing thousands of sequence variants to pinpoint the functional features within the SIRLOIN element, which dictates nuclear enrichment through hnRNPK recruitment. In addition, we profiled the endogenous SIRLOIN RNA-nucleoprotein complex and identified the nuclear RNA-binding proteins SLTM and SNRNP70 as novel SIRLOIN binders. Taken together, using massively parallel assays, we identified the features that dictate binding of hnRNPK, SLTM, and SNRNP70 to SIRLOIN and found that these factors are jointly required for SIRLOIN activity. Our study thus provides a roadmap for high-throughput dissection of functional sequence elements in long RNAs.
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