Post-transcriptional Regulatory Functions of Mammalian Pumilio Proteins

Goldstrohm, Aaron C.; Hall, Traci M. Tanaka; McKenney, Katherine M.

doi:10.1016/j.tig.2018.09.006

Cited by 152 publications

(190 citation statements)

References 120 publications

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“…Pum orthologs in other species. Drosophila Pum serves as an archetype, and the conservation of its repressive domains, including those in its N-terminus and RBD, in animals ranging from insects to vertebrates indicates that the mechanisms and co-repressors described here will be relevant (47). Indeed, as noted above, accumulating evidence supports the role of deadenylation, decapping, and translational inhibition in Pum repression in multiple model organisms.…”

Section: The Mechanistic Insights Into Pum-mediated Repression Also Hmentioning

confidence: 64%

Unique repression domains of Pumilio utilize deadenylation and decapping factors to accelerate destruction of target mRNAs

Arvola

Chang

Buytendorp

et al. 2019

Preprint

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Pumilio is an RNA-binding protein that represses a network of mRNAs to control embryogenesis, stem cell fate, fertility, and neurological functions in Drosophila. We sought to identify the mechanism of Pumilio-mediated repression and find that it accelerates degradation of target mRNAs, mediated by three N-terminal Repression Domains (RDs), which are unique to Pumilio orthologs. We show that the repressive activities of the Pumilio RDs depend on specific subunits of the Ccr4-Not (CNOT) deadenylase complex. Depletion of Pop2, Not1, Not2, or Not3 subunits alleviates Pumilio RD-mediated repression of protein expression and mRNA decay, whereas depletion of other CNOT components had little or no effect. Moreover, the catalytic activity of Pop2 deadenylase is important for Pumilio RD activity. Further, we show that the Pumilio RDs directly bind to the CNOT complex. We also report that the decapping enzyme, Dcp2, participates in repression by the N-terminus of Pumilio. These results support a model wherein Pumilio utilizes CNOT deadenylase and decapping complexes to accelerate destruction of target mRNAs. Because the N-terminal RDs are conserved in mammalian Pumilio orthologs, the results of this work broadly enhance our understanding of Pumilio function and roles in diseases including cancer, neurodegeneration, and epilepsy.

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Section: The Mechanistic Insights Into Pum-mediated Repression Also Hmentioning

confidence: 64%

Unique repression domains of Pumilio utilize deadenylation and decapping factors to accelerate destruction of target mRNAs

Arvola

Chang

Buytendorp

et al. 2019

Preprint

Self Cite

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“…The RNA-MaP platform allows direct, parallel equilibrium and kinetic measurements of binding of thousands of RNAs with their RNA or protein interaction partners. Here we used RNA-MaP to determine the stabilities of a library of over 1000 RNA hairpin constructs, by quantifying the extent to which structure formation inhibits binding of the well-characterized single-stranded RNA binding proteins PUM1 and PUM2 (22)(23)(24)(25)(26)(27). Our results reveal substantial and systematic deviations between structure stabilities predicted by current algorithms and measured stabilities.…”

Section: Introductionmentioning

confidence: 95%

Quantitative high-throughput tests of ubiquitous RNA secondary structure prediction algorithms via RNA/protein binding

Becker

Jarmoskaite²,

Kappel

et al. 2019

Preprint

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Nearest-neighbor (NN) rules provide a simple and powerful quantitative framework for RNA structure prediction that is strongly supported for canonical Watson-Crick duplexes from a plethora of thermodynamic measurements. Predictions of RNA secondary structure based on nearest-neighbor (NN) rules are routinely used to understand biological function and to engineer and control new functions in biotechnology. However, NN applications to RNA structural features such as internal and terminal loops rely on approximations and assumptions, with sparse experimental coverage of the vast number of possible sequence and structural features.To test to what extent NN rules accurately predict thermodynamic stabilities across RNAs with non-WC features, we tested their predictions using a quantitative high-throughput assay platform, RNA-MaP. Using a thermodynamic assay with coupled protein binding, we carried out equilibrium measurements for over 1000 RNAs with a range of predicted secondary structure stabilities. Our results revealed substantial scatter and systematic deviations between NN predictions and observed stabilities. Solution salt effects and incorrect or omitted loop parameters contribute to these observed deviations. Our results demonstrate the need to independently and quantitatively test NN computational algorithms to identify their capabilities and limitations. RNA-MaP and related approaches can be used to test computational predictions and can be adapted to obtain experimental data to improve RNA secondary structure and other prediction algorithms. Significance statementRNA secondary structure prediction algorithms are routinely used to understand, predict and design functional RNA structures in biology and biotechnology. Given the vast number of RNA sequence and structural features, these predictions rely on a series of approximations, and independent tests are needed to quantitatively evaluate the accuracy of predicted RNA structural stabilities. Here we measure the stabilities of over 1000 RNA constructs by using a coupled protein binding assay. Our results reveal substantial deviations from the RNA stabilities predicted by popular algorithms, and identify factors contributing to the observed deviations. We demonstrate the importance of quantitative, experimental tests of computational RNA structure predictions and present an approach that can be used to routinely test and improve the prediction accuracy.

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“…PTGR requires the activity of RNA-binding proteins, such as the widely-studied pumilio (PUM) proteins which are founding members of the PUF (pumilio and fem-3 binding factor) family of eukaryotic RNA-binding proteins. PUM proteins are highly conserved and present in many organisms, from yeast to humans (for review see (Goldstrohm, Hall et al, 2018)). Simultaneous knockout of mouse PUM1 and PUM2 is lethal (Zhang, Chen et al, 2017), indicating their crucial role in development.…”

Section: Introductionmentioning

confidence: 99%

Human PUM1 and PUM2 exhibit regulation of divergent mRNA targets in male germ cells

Ilaslan

et al. 2019

Preprint

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Mammalian Pumilio (PUM) proteins are sequence-specific, RNA-binding proteins with wideranging roles, including germ cell development that has functional implications in fertility.Although human PUM1 and PUM2 are closely related to each other and recognize the same RNA binding motif, there is some evidence for functional diversity, particularly related to their roles in fertility. Here, by RNA sequencing (RNA-Seq) approaches, we identified separate mRNA pools regulated by PUM1 and PUM2 proteins in human male germ cells.Using global mass spectrometry-based profiling, we identified distinct PUM1-and PUM2bound putative protein cofactors, most of them involved in RNA processing. Combinatorial analysis of RNA-Seq and mass spectrometry findings revealed that PUM1 and PUM2 may form distinct RNA-regulatory networks, with different roles in human reproduction and testicular tumorigenesis. Our findings highlight the functional divergence and versatility of PUM paralogue-based post-transcriptional regulation, offering insight into the mechanisms underlying their diverse biological roles and diseases resulting from their dysfunction.

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Post-transcriptional Regulatory Functions of Mammalian Pumilio Proteins

Cited by 152 publications

References 120 publications

Unique repression domains of Pumilio utilize deadenylation and decapping factors to accelerate destruction of target mRNAs

Unique repression domains of Pumilio utilize deadenylation and decapping factors to accelerate destruction of target mRNAs

Quantitative high-throughput tests of ubiquitous RNA secondary structure prediction algorithms via RNA/protein binding

Human PUM1 and PUM2 exhibit regulation of divergent mRNA targets in male germ cells

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