Suchergebnisse

SUMMARY: Here we introduce ccSOL omics, a webserver for large-scale calculations of protein solubility. Our method allows (i) proteome-wide predictions; (ii) identification of soluble fragments within each sequences; (iii) exhaustive single-point mutation analysis. RESULTS: Using coil/disorder, hydrophobicity, hydrophilicity, β-sheet and α-helix propensities, we built a predictor of protein solubility. Our approach shows an accuracy of 79% on the training set (36 990 Target Track entries). Validation on three independent sets indicates that ccSOL omics discriminates soluble and insoluble proteins with an accuracy of 74% on 31 760 proteins sharing <30% sequence similarity. AVAILABILITY AND IMPLEMENTATION: ccSOL omics can be freely accessed on the web at http://s.tartaglialab.com/page/ccsol_group. Documentation and tutorial are available at http://s.tartaglialab.com/static_files/shared/tutorial_ccsol_omics.html. CONTACT: gian.tartaglia@crg.es/nSUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. ; The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007–2013), through the European Research Council,under grant agreement RIBOMYLOME 309545, and from the Spanish Ministry of Economy and Competitiveness (SAF2011-26211). We also acknowledge support from the Spanish Ministry of Economy and Competitiveness, 'Centro de Excelencia Severo Ochoa 2013–2017' (SEV-2012-0208)

The biological function of multiple repetitions of single amino acids, or homo-repeats, is largely unknown, but their occurrence in proteins has been associated with more than 20 hereditary diseases. Analysing 122 bacterial and eukaryotic genomes, we observed that the number of proteins containing homo-repeats is significantly larger than expected from theoretical estimates. Analysis of statistical significance indicates that the minimal size of homo-repeats varies with amino acid type and proteome. In an attempt to characterize proteins harbouring long homo-repeats, we found that those containing polar or small amino acids S, P, H, E, D, K, Q and N are enriched in structural disorder as well as protein- and RNA-interactions. We observed that E, S, Q, G, L, P, D, A and H homo-repeats are strongly linked with occurrence in human diseases. Moreover, S, E, P, A, Q, D and T homo-repeats are significantly enriched in neuronal proteins associated with autism and other disorders. We release a webserver for further exploration of homo-repeats occurrence in human pathology at http://bioinfo.protres.ru/hradis/. ; This study was supported by the Russian Science Foundation grant number 14-14-00536 for OVG and the programs "Molecular and Cellular Biology" (01201353567) for MYL and IVS. GGT received funding from the European Union Seventh Framework Programme (FP7/2007–2013), through the European Research Council, under grant agreement RIBOMYLOME_309545, and from the Spanish Ministry of Economy and Competitiveness. PK and GGT also acknowledge support from the Spanish Ministry of Economy and Competitiveness, 'Centro de Excelencia Severo Ochoa 2013–2017' (SEV-2012-0208). PK is recipient of a "La Caixa" studentship.

From transcription, to transport, storage, and translation, RNA depends on association with different RNA-binding proteins (RBPs). Methods based on next-generation sequencing and protein mass-spectrometry have started to unveil genome-wide interactions of RBPs but many aspects still remain out of sight. How many of the binding sites identified in high-throughput screenings are functional? A number of computational methods have been developed to analyze experimental data and to obtain insights into the specificity of protein–RNA interactions. How can theoretical models be exploited to identify RBPs? In addition to oligomeric complexes, protein and RNA molecules can associate into granular assemblies whose physical properties are still poorly understood. What protein features promote granule formation and what effects do these assemblies have on cell function? Here, we describe the newest in silico, in vitro, and in vivo advances in the field of protein–RNA interactions. We also present the challenges that experimental and computational approaches will have to face in future studies. WIREs RNA 2016, 7:793–810. doi:10.1002/wrna.1378 ; The research leading to this work has received funding from the European Union Seventh Framework Programme (FP7/2007-2013), through the European Research Council, under grant agreement RIBOMYLOME_309545 (Gian Gaetano Tartaglia), and from the Spanish Ministry of Economy and Competitiveness (BFU2014-55054-P). We also acknowledge support from AGAUR (2014 SGR 00685) and the Spanish Ministry of Economy and Competitiveness 'Centro de Excelencia Severo Ochoa 2013–2017' (SEV-2012-0208).

RNA-binding proteins (RBPs) are crucial factors of post-transcriptional gene regulation and their modes of action are intensely investigated. At the center of attention are RNA motifs that guide where RBPs bind. However, sequence motifs are often poor predictors of RBP-RNA interactions in vivo. It is hence believed that many RBPs recognize RNAs as complexes, to increase specificity and regulatory possibilities. To probe the potential for complex formation among RBPs, we assembled a library of 978 mammalian RBPs and used rec-Y2H matrix screening to detect direct interactions between RBPs, sampling > 600 K interactions. We discovered 1994 new interactions and demonstrate that interacting RBPs bind RNAs adjacently in vivo. We further find that the mRNA binding region and motif preferences of RBPs deviate, depending on their adjacently binding interaction partners. Finally, we reveal novel RBP interaction networks among major RNA processing steps and show that splicing impairing RBP mutations observed in cancer rewire spliceosomal interaction networks. The dataset we provide will be a valuable resource for understanding the combinatorial interactions of RBPs with RNAs and the resulting regulatory outcomes. ; Spanish Ministry of Economy and Competitiveness (MINECO) [BFU2017-85361-P, BFU2014-54278-P, BFU2015-62550-ERC]; Spanish Ministry of Economy and Competitiveness to the EMBL partnership, 'Centro de Excelencia Severo Ochoa' [SEV-2012–0208 and SEV‐2015‐0533]; Spanish Ministry of Science and Innovation-State Research Agency (AEI), through the 'Severo Ochoa Programme for Centres of Excellence in R&D' [SEV-2015-0533 and CEX2019-000902-S]; CERCA Programme/Generalitat de Catalunya; European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie [793135 to B.L.]. Funding for open access charge: Ministerio de Economía y Competitividad. ; Peer reviewed

RNA-binding proteins (RBPs) are crucial factors of post-transcriptional gene regulation and their modes of action are intensely investigated. At the center of attention are RNA motifs that guide where RBPs bind. However, sequence motifs are often poor predictors of RBP-RNA interactions in vivo. It is hence believed that many RBPs recognize RNAs as complexes, to increase specificity and regulatory possibilities. To probe the potential for complex formation among RBPs, we assembled a library of 978 mammalian RBPs and used rec-Y2H matrix screening to detect direct interactions between RBPs, sampling > 600 K interactions. We discovered 1994 new interactions and demonstrate that interacting RBPs bind RNAs adjacently in vivo. We further find that the mRNA binding region and motif preferences of RBPs deviate, depending on their adjacently binding interaction partners. Finally, we reveal novel RBP interaction networks among major RNA processing steps and show that splicing impairing RBP mutations observed in cancer rewire spliceosomal interaction networks. The dataset we provide will be a valuable resource for understanding the combinatorial interactions of RBPs with RNAs and the resulting regulatory outcomes. ; Spanish Ministry of Economy and Competitiveness (MINECO) [BFU2017-85361-P, BFU2014-54278-P, BFU2015-62550-ERC]; Spanish Ministry of Economy and Competitiveness to the EMBL partnership, 'Centro de Excelencia Severo Ochoa' [SEV-2012–0208 and SEV‐2015‐0533]; Spanish Ministry of Science and Innovation-State Research Agency (AEI), through the 'Severo Ochoa Programme for Centres of Excellence in R&D' [SEV-2015-0533 and CEX2019-000902-S]; CERCA Programme/Generalitat de Catalunya; European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie [793135 to B.L.]. Funding for open access charge: Ministerio de Economía y Competitividad.

Introduction: Genome-wide association studies (GWAS) in late onset Alzheimer's disease (LOAD) provide lists of individual genetic determinants. However, GWAS do not capture the synergistic effects among multiple genetic variants and lack good specificity. Methods: We applied tree-based machine learning algorithms (MLs) to discriminate LOAD (>700 individuals) and age-matched unaffected subjects in UK Biobank with single nucleotide variants (SNVs) from Alzheimer's disease (AD) studies, obtaining specific genomic profiles with the prioritized SNVs. Results: MLs prioritized a set of SNVs located in genes PVRL2, TOMM40, APOE, and APOC1, also influencing gene expression and splicing. The genomic profiles in this region showed interaction patterns involving rs405509 and rs1160985, also present in the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset. rs405509 located in APOE promoter interacts with rs429358 among others, seemingly neutralizing their predisposing effect. Discussion: Our approach efficiently discriminates LOAD from controls, capturing genomic profiles defined by interactions among SNVs in a hot-spot region. ; Funding: the research leading to these results was supported by the European Union's Horizon 2020 research and innovation programme under grant agreement No. 727658 (project iASiS), European Research Council ASTRA 855923, and the European Genome‐phenome Archive (EGA). Claudia Giambartolomei has received funding from the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska‐Curie grant agreement No 754490–MINDED project. This research has been conducted using the UK Biobank Resource under Application Number 35916

We thank the "RNA Initiative" at IIT, all members of the M.H.H., A.P., and G.G.T. groups, and especially Fernando Cid Samper. M.H.H. wishes to thank UCB Biopharma and Dr Jim Love for providing funding for the instrument used to generate the super-resolution data in this manuscript. A.P. acknowledges funding from UK DRI (grant REI 3556) and AlzheimerUK (grant ARUK-PG2019B-020). O.K. was supported by a Scottish PhD Research & Innovation Network Traineeships in MND/MS. E.Z. received funding from the Newton fellowship scheme and the MINDED fellowship of the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No. 754490. K.J. was funded via the BBSRCEastBIO doctoral training program (BB/M010996/1). The research leading to these results was supported by European Research Council [RIBOMYLOME n. 309545 to G.G.T. and ASTRA n. 855923 to G.G.T.], H2020 [IASIS n. 727658 to G.G.T. and INFORE n. 825080 to G.G.T.] and MND [840-791 to G.G.T. and A.P.] projects. The authors would also like to acknowledge the help and support received during confocal images acquisition by the group of Giuseppe Vicidomini at the Molecular Microscopy and Spectroscopy Department of IIT. ; Peer reviewed ; Publisher PDF

The mechanisms by which mutations in FUS and other RNA binding proteins cause ALS and FTD remain controversial. We propose a model in which low-complexity (LC) domains of FUS drive its physiologically reversible assembly into membrane-free, liquid droplet and hydrogel-like structures. ALS/FTD mutations in LC or non-LC domains induce further phase transition into poorly soluble fibrillar hydrogels distinct from conventional amyloids. These assemblies are necessary and sufficient for neurotoxicity in a C. elegans model of FUS-dependent neurodegeneration. They trap other ribonucleoprotein (RNP) granule components and disrupt RNP granule function. One consequence is impairment of new protein synthesis by cytoplasmic RNP granules in axon terminals, where RNP granules regulate local RNA metabolism and translation. Nuclear FUS granules may be similarly affected. Inhibiting formation of these fibrillar hydrogel assemblies mitigates neurotoxicity and suggests a potential therapeutic strategy that may also be applicable to ALS/FTD associated with mutations in other RNA binding proteins. ; Supported by Canadian Institutes of Health Research (PEF, PStGH), Alzheimer Society of Ontario (PEF, PStGH), Wellcome Trust (PStGH, MEV, CFK, GSK, DR, CEH), Medical Research Council (PStGH, MEV, CFK, GSK), National Institutes of Health Research, Alzheimer Research UK (CFK, GSK), Gates Cambridge Scholarship (JQL), Engineering and Physical Sciences Research Council (CFK, GSK), European Research Council Starting Grant RIBOMYLOME_309545 (GGT), European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013) / ERC Grant Agreement no. 322817 (CEH), and National Institute of Neurological Disorders and Stroke R01 NS07377 (NAS). The authors thank Tom Cech and Roy Parker for helpful discussions. ; This is the final version of the article. It was first available from Elsevier via http://dx.doi.org/10.1016/j.neuron.2015.10.030