Neurodegenerative diseases: Quantitative predictions of protein–RNA interactions

Cirillo, Davide; Federico, Antonella; Klus, Petr; Marchese, Domenica; Rodríguez, Sergio; Bolognesi, Benedetta; Tartaglia, Gian Gaetano

doi:10.1261/rna.034777.112

Cited by 70 publications

(93 citation statements)

References 57 publications

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“…Indeed, amyloidogenic proteins such as TDP-43 and FMRP (Reactome pathway ‘Amyloids’) have strong propensities to bind to their mRNAs and have been discussed in our previous work (5). …”

Section: Resultsmentioning

confidence: 97%

“…Recent studies showed that establishment of aberrant associations or disruption of functional protein–RNA interactions occurs in neurological disorders (5,6). For instance, interaction with RNA favors conversion of alpha-helix rich prion protein PrP C into the pathogenic beta-structure-rich insoluble conformer PrP Sc that propagates in Creutzfeldt–Jakob disease (7).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Principles of self-organization in biological pathways: a hypothesis on the autogenous association of alpha-synuclein

Zanzoni¹,

Marchese²,

Federico³

et al. 2013

Nucleic Acids Research

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Previous evidence indicates that a number of proteins are able to interact with cognate mRNAs. These autogenous associations represent important regulatory mechanisms that control gene expression at the translational level. Using the catRAPID approach to predict the propensity of proteins to bind to RNA, we investigated the occurrence of autogenous associations in the human proteome. Our algorithm correctly identified binding sites in well-known cases such as thymidylate synthase, tumor suppressor P53, synaptotagmin-1, serine/ariginine-rich splicing factor 2, heat shock 70 kDa, ribonucleic particle-specific U1A and ribosomal protein S13. In addition, we found that several other proteins are able to bind to their own mRNAs. A large-scale analysis of biological pathways revealed that aggregation-prone and structurally disordered proteins have the highest propensity to interact with cognate RNAs. These findings are substantiated by experimental evidence on amyloidogenic proteins such as TAR DNA-binding protein 43 and fragile X mental retardation protein. Among the amyloidogenic proteins, we predicted that Parkinson’s disease-related α-synuclein is highly prone to interact with cognate transcripts, which suggests the existence of RNA-dependent factors in its function and dysfunction. Indeed, as aggregation is intrinsically concentration dependent, it is possible that autogenous interactions play a crucial role in controlling protein homeostasis.

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“…Indeed, amyloidogenic proteins such as TDP-43 and FMRP (Reactome pathway ‘Amyloids’) have strong propensities to bind to their mRNAs and have been discussed in our previous work (5). …”

Section: Resultsmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

Principles of self-organization in biological pathways: a hypothesis on the autogenous association of alpha-synuclein

Zanzoni¹,

Marchese²,

Federico³

et al. 2013

Nucleic Acids Research

Self Cite

View full text Add to dashboard Cite

show abstract

“…However, when tested on 12,000 randomly generated RNA associations with proteins extracted from a non-Nucleic Acid-binding dataset [19], ~ 30% of these were predicted to interact with RNA [17]. In a recent study [20], the authors used catRAPID to investigate ribonucleoprotein interactions linked to neurodegenerative diseases. An advantage of the catRAPID algorithm is that it is the only published method that simultaneously predicts the binding sites in both RNA and protein sequences [21].…”

Section: Rna-protein Partner Prediction Methods and Web Serversmentioning

confidence: 99%

“…As discussed above, catRAPID predicts interaction partners based on the interaction propensities of individual residues [17]. In several cases, catRAPID binding site predictions correlate well with experimental results [20,33], but the performance of this method has not been evaluated systematically on benchmark datasets. Therefore, it is difficult to comment on the relative accuracy of this method in predicting interfacial residues in either RNA or protein sequences.…”

Section: Rna-protein Interface Prediction Methodsmentioning

confidence: 99%

Computational Tools for Investigating RNA-Protein Interaction Partners

Muppirala¹,

Lewis

Dobbs

2013

J Comput Sci Syst Biol

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RNA-protein interactions are important in a wide variety of cellular and developmental processes. Recently, high-throughput experiments have begun to provide valuable information about RNA partners and binding sites for many RNA-binding proteins (RBPs), but these experiments are expensive and time consuming. Thus, computational methods for predicting RNA-Protein interactions (RPIs) can be valuable tools for identifying potential interaction partners of a given protein or RNA, and for identifying likely interfacial residues in RNAprotein complexes. This review focuses on the "partner prediction" problem and summarizes available computational methods, web servers and databases that are devoted to it. New computational tools for addressing the related "interface prediction" problem are also discussed. Together, these computational methods for investigating RNA-protein interactions provide the basis for new strategies for integrating RNAprotein interactions into existing genetic and developmental regulatory networks, an important goal of future research.

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“…The cat RAPID algorithm has been previously validated on a number of protein–RNA associations (Agostini et al , 2013; Bellucci et al , 2011; Cirillo, et al , 2013a; Johnson et al , 2012). To evaluate large-scale performances of cat RAPID omics , we used data from recent large-scale experiments.…”

Section: Performancesmentioning

confidence: 99%

catRAPID omics: a web server for large-scale prediction of protein–RNA interactions

et al. 2013

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Summary: Here we introduce catRAPID omics, a server for large-scale calculations of protein–RNA interactions. Our web server allows (i) predictions at proteomic and transcriptomic level; (ii) use of protein and RNA sequences without size restriction; (iii) analysis of nucleic acid binding regions in proteins; and (iv) detection of RNA motifs involved in protein recognition.Results: We developed a web server to allow fast calculation of ribonucleoprotein associations in Caenorhabditis elegans, Danio rerio, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae and Xenopus tropicalis (custom libraries can be also generated). The catRAPID omics was benchmarked on the recently published RNA interactomes of Serine/arginine-rich splicing factor 1 (SRSF1), Histone-lysine N-methyltransferase EZH2 (EZH2), TAR DNA-binding protein 43 (TDP43) and RNA-binding protein FUS (FUS) as well as on the protein interactomes of U1/U2 small nucleolar RNAs, X inactive specific transcript (Xist) repeat A region (RepA) and Crumbs homolog 3 (CRB3) 3′-untranslated region RNAs. Our predictions are highly significant (P < 0.05) and will help the experimentalist to identify candidates for further validation.Availability: catRAPID omics can be freely accessed on the Web at http://s.tartaglialab.com/catrapid/omics. Documentation, tutorial and FAQs are available at http://s.tartaglialab.com/page/catrapid_group.Contact: gian.tartaglia@crg.eu

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Neurodegenerative diseases: Quantitative predictions of protein–RNA interactions

Cited by 70 publications

References 57 publications

Principles of self-organization in biological pathways: a hypothesis on the autogenous association of alpha-synuclein

Principles of self-organization in biological pathways: a hypothesis on the autogenous association of alpha-synuclein

Computational Tools for Investigating RNA-Protein Interaction Partners

catRAPID omics: a web server for large-scale prediction of protein–RNA interactions

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