Alternative 3′ UTRs act as scaffolds to regulate membrane protein localization

Berkovits, Binyamin D.; Mayr, Christine

doi:10.1038/nature14321

Cited by 474RNA Research and SplicingRNA and protein synthesis mechanismsRNA regulation and disease

Alternative 3′ UTRs act as scaffolds to regulate membrane protein localization

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Berkovits, Binyamin D., Mayr, Christine·2015·Nature

DOI 10.1038/nature14321PMC PMC4697748

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Abstract

About half of human genes use alternative cleavage and polyadenylation (ApA) to generate messenger RNA transcripts that differ in the length of their 3' untranslated regions (3' UTRs) while producing the same protein. Here we show in human cell lines that alternative 3' UTRs differentially regulate the localization of membrane proteins. The long 3' UTR of CD47 enables efficient cell surface expression of CD47 protein, whereas the short 3' UTR primarily localizes CD47 protein to the endoplasmic reticulum. CD47 protein localization occurs post-translationally and independently of RNA localization. In our model of 3' UTR-dependent protein localization, the long 3' UTR of CD47 acts as a scaffold to recruit a protein complex containing the RNA-binding protein HuR (also known as ELAVL1) and SET to the site of translation. This facilitates interaction of SET with the newly translated cytoplasmic domains of CD47 and results in subsequent translocation of CD47 to the plasma membrane via activated RAC1 (ref. 5). We also show that CD47 protein has different functions depending on whether it was generated by the short or long 3' UTR isoforms. Thus, ApA contributes to the functional diversity of the proteome without changing the amino acid sequence. 3' UTR-dependent protein localization has the potential to be a widespread trafficking mechanism for membrane proteins because HuR binds to thousands of mRNAs, and we show that the long 3' UTRs of CD44, ITGA1 and TNFRSF13C, which are bound by HuR, increase surface protein expression compared to their corresponding short 3' UTRs. We propose that during translation the scaffold function of 3' UTRs facilitates binding of proteins to nascent proteins to direct their transport or function--and this role of 3' UTRs can be regulated by ApA.

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The 5′ and 3′ UTRs flanking the coding region regulate mRNA translation, half-life and subcellular localization.
“The 5′ and 3′ UTRs flanking the coding region regulate mRNA translation, half-life and subcellular localization10,14.”
From mRNA vaccines for infectious diseases: principles, delivery and clinical translation (2021) · cites this paper as [14]

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Authors: Berkovits, B. D., & Mayr, C.
Affiliations: Memorial Sloan Kettering Cancer Center (US)
Corresponding author: Mayr, Christine
ORCID: Mayr, Christine
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2015-04-20
Volume: 522
Issue: 7556
Pages: 363-367
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature14321
PMC: PMC4697748
OpenAlex: W1969412365
Cited by: 474
References: 39
Citations by year: 2026: 26 · 2025: 40 · 2024: 39 · 2023: 42 · 2022: 38 · 2021: 75 · 2020: 47 · 2019: 50 · 2018: 38 · 2017: 38 · 2016: 28 · 2015: 11 · 2014: 1
FWCI: 16.54
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.springer.com/tdm (tdm)
Locations: Nature (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
RePEc: Research Papers in Economics (submittedVersion)
Funders: Damon Runyon Cancer Research Foundation (DRR-24-13)
National Cancer Institute (U01CA164190, P30CA008748)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
Keywords: 3' untranslated region, CD47, membrane protein localization, HuR, Rac1, post-translational translocation, endoplasmic reticulum, cell surface expression, mRNA isoforms, alternative splicing, phagocytosis resistance, RNA-binding proteins, translational regulation, protein scaffolds
MeSH terms: ELAV-Like Protein 1, Cell Line, Cell Membrane, DNA-Binding Proteins, Endoplasmic Reticulum, Humans, Membrane Proteins, RNA, Messenger, Transcription Factors, Genes, Reporter, 3' Untranslated Regions, rac1 GTP-Binding Protein, Protein Transport, Polyadenylation, CD47 Antigen, ELAV Proteins, Histone Chaperones, RNA Isoforms

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Alternative 3′ UTRs act as scaffolds to regulate membrane protein localization

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