Specific length and structure rather than high thermodynamic stability enable regulatory mRNA stem-loops to pause translation

Bao, Chen; Zhu, Mingyi; Nykonchuk, Inna; Wakabayashi, Hironao; Mathews, David H.; Ermolenko, Dmitri N.

doi:10.1101/2021.08.16.456581

Cited by 4 publications

(2 citation statements)

References 74 publications

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“…5I) that is not evident in the global duplexes detected by PARIS. This requirement for specific lengths and structural conformations, rather than thermodynamic stability, to enable regulatory function is reminiscent of one recently described in the context of ribosome stalling (29).…”

Section: Resultsmentioning

confidence: 79%

A computationally-enhanced hiCLIP atlas reveals Staufen1 RNA binding features and links 3’ UTR structure to RNA metabolism

Chakrabarti

Iosub

Lee

et al. 2022

Preprint

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The structure of mRNA molecules plays an important role in its interactions with trans-acting factors, notably RNA binding proteins (RBPs), thus contributing to the functional consequences of this interplay. However, current transcriptome-wide experimental methods to chart these interactions are limited by their poor sensitivity. Here we extend the hiCLIP atlas of duplexes bound by Staufen1 (STAU1) ~10-fold, through careful consideration of experimental assumptions, and the development of bespoke computational methods which we apply to existing data. We present Tosca, a Nextflow computational pipeline for the processing, analysis and visualisation of proximity ligation sequencing data generally. We use our extended duplex atlas to discover insights into the RNA selectivity of STAU1, revealing the importance of structural symmetry and duplex-span-dependent nucleotide composition. Furthermore, we identify heterogeneity in the relationship between STAU1-bound 3' UTRs and metabolism of the associated RNAs that we relate to RNA structure: transcripts with short-range proximal 3' UTR duplexes have high degradation rates, but those with long-range duplexes have low rates. Overall, our work enables the integrative analysis of proximity ligation data delivering insights into specific features and effects of RBP-RNA structure interactions.

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Section: Resultsmentioning

confidence: 79%

A computationally-enhanced hiCLIP atlas reveals Staufen1 RNA binding features and links 3’ UTR structure to RNA metabolism

Chakrabarti

Iosub

Lee

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…Although folding models suggest that m1 and m1m5 have equivalent potential to sequester the annotated site, the strong cryptic site in m1m5 may be disfavored for residual splicing, either because it is slightly weaker than m1 or because m1m5 itself becomes partially sequestered in stem 3 (Figure 4). A caveat to these interpretations is that secondary structure has a complex role in alternative splicing [12], and the predicted stability of stem loop structures may not be as critical as specific structures in determining RNA functionality [40].…”

Section: Discussionmentioning

confidence: 99%

A Deep Exon Cryptic Splice Site Promotes Aberrant Intron Retention in a Von Willebrand Disease Patient

Conboy

2021

IJMS

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A translationally silent single nucleotide mutation in exon 44 (E44) of the von Willebrand factor (VWF) gene is associated with inefficient removal of intron 44 in a von Willebrand disease (VWD) patient. This intron retention (IR) event was previously attributed to reordered E44 secondary structure that sequesters the normal splice donor site. We propose an alternative mechanism: the mutation introduces a cryptic splice donor site that interferes with the function of the annotated site to favor IR. We evaluated both models using minigene splicing reporters engineered to vary in secondary structure and/or cryptic splice site content. Analysis of splicing efficiency in transfected K562 cells suggested that the mutation-generated cryptic splice site in E44 was sufficient to induce substantial IR. Mutations predicted to vary secondary structure at the annotated site also had modest effects on IR and shifted the balance of residual splicing between the cryptic site and annotated site, supporting competition among the sites. Further studies demonstrated that introduction of cryptic splice donor motifs at other positions in E44 did not promote IR, indicating that interference with the annotated site is context dependent. We conclude that mutant deep exon splice sites can interfere with proper splicing by inducing IR.

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A deep exon cryptic splice site promotes aberrant intron retention in a von Willebrand disease patient

Conboy

2021

Preprint

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A translationally silent single nucleotide mutation, in exon 44 of the von Willebrand factor (VWF) gene, is associated with inefficient removal of intron 44 in a von Willebrand disease (VWD) patient. This intron retention (IR) event was previously attributed to altered secondary structure that sequesters the normal splice donor site. We propose an alternative mechanism: that the mutation introduces a cryptic splice donor site that interferes with function of the annotated site to favor IR. We evaluated both models using minigene splicing reporters engineered to vary in secondary structure and/or cryptic splice site content. Analysis of reporter splicing efficiency in transfected K562 cells suggested that the mutation-generated internal splice site was sufficient to induce substantial IR. Mutations predicted to vary secondary structure at the annotated site had modest effects on IR, and also shifted the balance of residual splicing between the cryptic site and annotated site, supporting competition between the sites. Further studies demonstrated that introduction of cryptic splice donor motifs at other positions in E44 did not promote IR, indicating that interference with the annotated site is context-dependent. We conclude that mutant deep exon splice sites can interfere with proper splicing by inducing IR.

show abstract

Specific length and structure rather than high thermodynamic stability enable regulatory mRNA stem-loops to pause translation

Cited by 4 publications

References 74 publications

A computationally-enhanced hiCLIP atlas reveals Staufen1 RNA binding features and links 3’ UTR structure to RNA metabolism

A computationally-enhanced hiCLIP atlas reveals Staufen1 RNA binding features and links 3’ UTR structure to RNA metabolism

A Deep Exon Cryptic Splice Site Promotes Aberrant Intron Retention in a Von Willebrand Disease Patient

A deep exon cryptic splice site promotes aberrant intron retention in a von Willebrand disease patient

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