The end of the message: multiple protein–RNA interactions define the mRNA polyadenylation site

Shi, Yongsheng; Manley, James L.

doi:10.1101/gad.261974.115

Cited by 230 publications

(238 citation statements)

References 108 publications

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“…Most hnRNP family members have been shown to regulate alternative splicing as well as other RNA processing steps such as 3 ′ end processing, mRNA translation, and mRNA stability (Bomsztyk et al 2004;Martinez-Contreras et al 2007;Licatalosi et al 2008). Moreover, global comparisons of transcriptomewide binding of individual hnRNPs with their effect on transcriptome expression have led to the general model that the functional consequence of a particular hnRNP on a given transcript is highly dependent on where it binds within an RNA (Licatalosi and Darnell 2009;Fu and Ares 2014;Shi and Manley 2015).…”

Section: Introductionmentioning

confidence: 99%

Global analysis of physical and functional RNA targets of hnRNP L reveals distinct sequence and epigenetic features of repressed and enhanced exons

Cole

Tapescu

Allon

et al. 2015

RNA

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HnRNP L is a ubiquitous splicing-regulatory protein that is critical for the development and function of mammalian T cells. Previous work has identified a few targets of hnRNP L-dependent alternative splicing in T cells and has described transcriptome-wide association of hnRNP L with RNA. However, a comprehensive analysis of the impact of hnRNP L on mRNA expression remains lacking. Here we use next-generation sequencing to identify transcriptome changes upon depletion of hnRNP L in a model T-cell line. We demonstrate that hnRNP L primarily regulates cassette-type alternative splicing, with minimal impact of hnRNP L depletion on transcript abundance, intron retention, or other modes of alternative splicing. Strikingly, we find that binding of hnRNP L within or flanking an exon largely correlates with exon repression by hnRNP L. In contrast, exons that are enhanced by hnRNP L generally lack proximal hnRNP L binding. Notably, these hnRNP L-enhanced exons share sequence and context features that correlate with poor nucleosome positioning, suggesting that hnRNP may enhance inclusion of a subset of exons via a cotranscriptional or epigenetic mechanism. Our data demonstrate that hnRNP L controls inclusion of a broad spectrum of alternative cassette exons in T cells and suggest both direct RNA regulation as well as indirect mechanisms sensitive to the epigenetic landscape.

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Section: Introductionmentioning

confidence: 99%

Global analysis of physical and functional RNA targets of hnRNP L reveals distinct sequence and epigenetic features of repressed and enhanced exons

Cole

Tapescu

Allon

et al. 2015

RNA

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“…Polyadenylation is a 3′ end maturation step that all eukaryotic mRNAs (except histones) undergo (Fig. 2) (12). It involves endonucleolytic cleavage of the pre-mRNA followed by addition of a polyadenosine tail.…”

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confidence: 99%

“…One important Cys 3 His ZF protein is cleavage and polyadenylation specificity factor 30 (CPSF30) (2,12). CPSF30 contains five Cys 3 His domains.…”

mentioning

confidence: 99%

“…Polyadenylation occurs at a specific region of the pre-mRNA called the polyadenylation cleavage site (PAS). The PAS consists of an upstream element with the conserved sequence AAUAAA (also called the AU-hexamer), a stretch of bases where cleavage occurs, after which a conserved GU-rich or U-rich sequence is present (usually between 40-60 nt after the cleavage site) (12,13). CPSF73 is the endonuclease that cleaves the RNA; the roles of the other CPSF proteins are less clear (12,13).…”

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confidence: 99%

“…The PAS consists of an upstream element with the conserved sequence AAUAAA (also called the AU-hexamer), a stretch of bases where cleavage occurs, after which a conserved GU-rich or U-rich sequence is present (usually between 40-60 nt after the cleavage site) (12,13). CPSF73 is the endonuclease that cleaves the RNA; the roles of the other CPSF proteins are less clear (12,13). Initially, CPSF160 was identified as the protein within the CPSF complex that recognizes the AU-hexamer (14-16); however, two recent studies using cellbased methods found that CPSF160 does not play this role (17,18).…”

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confidence: 99%

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Cleavage and polyadenylation specificity factor 30: An RNA-binding zinc-finger protein with an unexpected 2Fe–2S cluster

Shimberg

Michalek

Oluyadi

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Cleavage and polyadenylation specificity factor 30 (CPSF30) is a key protein involved in pre-mRNA processing. CPSF30 contains five Cys 3 His domains (annotated as "zinc-finger" domains). Using inductively coupled plasma mass spectrometry, X-ray absorption spectroscopy, and UV-visible spectroscopy, we report that CPSF30 is isolated with iron, in addition to zinc. Iron is present in CPSF30 as a 2Fe-2S cluster and uses one of the Cys 3 His domains; 2Fe-2S clusters with a Cys 3 His ligand set are rare and notably have also been identified in MitoNEET, a protein that was also annotated as a zinc finger. These findings support a role for iron in some zinc-finger proteins. Using electrophoretic mobility shift assays and fluorescence anisotropy, we report that CPSF30 selectively recognizes the AU-rich hexamer (AAUAAA) sequence present in pre-mRNA, providing the first molecular-based evidence to our knowledge for CPSF30/RNA binding. Removal of zinc, or both zinc and iron, abrogates binding, whereas removal of just iron significantly lessens binding. From these data we propose a model for RNA recognition that involves a metaldependent cooperative binding mechanism.zinc | iron-sulfur | RNA | protein | binding

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RNA recognition by Roquin in posttranscriptional gene regulation

et al. 2016

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Posttranscriptional regulation of gene expression plays a central role in the initiation of innate and adaptive immune responses. This is exemplified by the protein Roquin, which has attracted great interest during the past decade owing to its ability to prevent autoimmunity. Roquin controls T-cell activation and T helper cell differentiation by limiting the induced expression of costimulatory receptors on the surface of T cells. It does so by recognizing cis regulatory RNA-hairpin elements in the 3' UTR of target transcripts via its ROQ domain-a novel RNA-binding fold-and triggering their degradation through recruitment of factors that mediate deadenylation and decapping. Recent structural studies have revealed molecular details of the recognition of RNA hairpin structures by the ROQ domain. Surprisingly, it was found that Roquin mainly relies on shape-specific recognition of the RNA. This observation implies that a much broader range of RNA motifs could interact with the protein, but it also complicates systematic searches for novel mRNA targets of Roquin. Thus, large-scale approaches, such as crosslinking and immunoprecipitation or systematic evolution of ligands by exponential enrichment experiments coupled with next-generation sequencing, will be required to identify the complete spectrum of its target RNAs. Together with structural analyses of their binding modes, this will enable us to unravel the intricate complexity of 3' UTR regulation by Roquin and other trans-acting factors. Here, we review our current understanding of Roquin-RNA interactions and their role for Roquin function. WIREs RNA 2016, 7:455-469. doi: 10.1002/wrna.1333 For further resources related to this article, please visit the WIREs website.

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The end of the message: multiple protein–RNA interactions define the mRNA polyadenylation site

Cited by 230 publications

References 108 publications

Global analysis of physical and functional RNA targets of hnRNP L reveals distinct sequence and epigenetic features of repressed and enhanced exons

Global analysis of physical and functional RNA targets of hnRNP L reveals distinct sequence and epigenetic features of repressed and enhanced exons

Cleavage and polyadenylation specificity factor 30: An RNA-binding zinc-finger protein with an unexpected 2Fe–2S cluster

RNA recognition by Roquin in posttranscriptional gene regulation

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