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catRAPIDsignature: identification of ribonucleoproteins and RNA-binding regions

Carmen Maria Livi, Petr Klus, Riccardo Delli Ponti, Gian Gaetano Tartaglia
2015 Bioinformatics  
algorithms in the identification of RNA-binding proteins and detection of non-classical RNA-binding regions.  ...  The algorithm, trained on human proteins and tested on model organisms, calculates the overall RNA-binding propensity followed by the prediction of RNA-binding regions. catRAPID signature outperforms other  ...  Funding: We thank the Spanish Ministry of Economy and Competitiveness (BFU2014-55054-P), the European Research Council (ERC Starting Grant "Ribomylome" 309545 to GGT).  ... 
doi:10.1093/bioinformatics/btv629 pmid:26520853 pmcid:PMC4795616 fatcat:n2aykgtr3nbe3jqmg5bxpbe47q

Advances in the characterization of RNA-binding proteins

Domenica Marchese, Natalia Sanchez de Groot, Nieves Lorenzo Gotor, Carmen Maria Livi, Gian G. Tartaglia
2016 Wiley Interdisciplinary Reviews - RNA  
From transcription, to transport, storage, and translation, RNA depends on association with different RNA-binding proteins (RBPs).  ...  How many of the binding sites identified in high-throughput screenings are functional?  ...  from the Spanish Ministry of Economy and Competitiveness (BFU2014-55054-P).  ... 
doi:10.1002/wrna.1378 pmid:27503141 pmcid:PMC5113702 fatcat:e6akw5hhsrgbhpvibod6hd6fpi

Neurodegenerative diseases: Quantitative predictions of protein-RNA interactions

D. Cirillo, F. Agostini, P. Klus, D. Marchese, S. Rodriguez, B. Bolognesi, G. G. Tartaglia
2012 RNA: A publication of the RNA Society  
We recently introduced a theoretical framework, catRAPID, to predict the binding ability of protein and RNA molecules.  ...  43 TDP-43; (4) autogenous regulation of TDP-43 and FMRP; (5) iron-mediated expression of amyloid precursor protein APP and α-synuclein; (6) interactions between prions and RNA aptamers.  ...  Lehner, and Viola Tartaglia for stimulating discussions. Our work was supported by the Spanish Ministry of Economy and Competitiveness (SAF2011-26211).  ... 
doi:10.1261/rna.034777.112 pmid:23264567 pmcid:PMC3543085 fatcat:zsirazykdbh47gldbxowxtnspm

A Computational Approach for the Discovery of Protein–RNA Networks [chapter]

Domenica Marchese, Carmen Maria Livi, Gian Gaetano Tartaglia
2016 Msphere  
In this chapter we present the computational approach catRAPID to predict protein-RNA interactions and discuss how it could be used to find trends in ribonucleoprotein networks.  ...  We envisage that the combination of computational and experimental approaches will be crucial to unravel the role of coding and non-coding RNAs in protein networks  ...  to identify RNA regions involved in protein binding.  ... 
doi:10.1007/978-1-4939-3067-8_2 pmid:26463375 fatcat:ckx2gnus7jfqlmrfhz5fbxp4ze

APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins

Malvika Sharan, Konrad U. Förstner, Ana Eulalio, Jörg Vogel
2017 Nucleic Acids Research  
Experimental techniques such as cross-linking and coimmunoprecipitation have enabled the identification of RBPs, RNA-binding domains (RBDs) and their regulatory roles in the eukaryotic species such as  ...  RNA-binding proteins (RBPs) have been established as core components of several posttranscriptional gene regulation mechanisms.  ...  ACKNOWLEDGEMENTS The authors thank the members of the Vogel group, Eulalio group and the Core Unit (CU) Systems Medicine, especially Dr Charlotte Michaux and Caroline Taouk for contributing into the project  ... 
doi:10.1093/nar/gkx137 pmid:28334975 pmcid:PMC5499795 fatcat:4evcr272hzdf7gwwwdc4v5rjxu

APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins [article]

Malvika Sharan, Konrad Ulrich Foerstner, Ana Eulalio, Joerg Vogel
2016 bioRxiv   pre-print
Experimental techniques such as cross-linking and co-immunoprecipitation have enabled the identification of RBPs, RNA-binding domains (RBDs), and their regulatory roles in the eukaryotic species such as  ...  RNA-binding proteins (RBPs) have been established as core components of several post-transcriptional gene regulation mechanisms.  ...  The fourth tool, catRAPID signature, is a SVM based method to identify RNA-binding proteins and their binding regions based on physico-chemical properties.  ... 
doi:10.1101/055178 fatcat:ekev5oq5kjcfzcq6qn7ysoh5ey

Integrated Analysis of Dysregulated lncRNA Expression in Fetal Cardiac Tissues with Ventricular Septal Defect

Guixian Song, Yahui Shen, Jingai Zhu, Hailang Liu, Ming Liu, Ya-Qing Shen, Shasha Zhu, Xiangqing Kong, Zhangbin Yu, Lingmei Qian, Qiong Wu
2013 PLoS ONE  
In the present study, we conducted an integrated analysis of dysregulated lncRNAs, focusing specifically on the identification and characterization of lncRNAs potentially involving in initiation of VSD  ...  Long noncoding RNAs (lncRNAs) have been shown to play key roles in various biological processes, such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and  ...  Further catRAPID analysis indicated a strong RNA-protein interaction between ENST0000051354 and TCF-4, a TF of SMAD1 (Figure 5 D) .  ... 
doi:10.1371/journal.pone.0077492 pmid:24147006 pmcid:PMC3797806 fatcat:hr7a73r2xrc2tkp4yezfmkjiea

Molecular Pathophysiology of Fragile X-Associated Tremor/Ataxia Syndrome and Perspectives for Drug Development

Teresa Botta-Orfila, Gian Gaetano Tartaglia, Aubin Michalon
2016 Cerebellum  
In this review we present the two most accepted toxicity mechanisms described so far, namely RNA gain-of-function and protein gain-of-function by means of repeatassociated non-AUG translation, and discuss  ...  Fragile X-associated tremor/ataxia syndrome (FXTAS) is an inherited neurodegenerative disorder manifesting in carriers of 55 to 200 CGG repeats in the 5' untranslated region (UTR) of the fragile X mental  ...  et al., , 2014 Zanzoni et al., 2013) Applied to the CGG repeat RNA, catRAPID predicted the sequestration of several proteins including MBNL1 and the heterogeneous nuclear ribonucleoproteins (hnRNP) A1  ... 
doi:10.1007/s12311-016-0800-2 pmid:27277287 fatcat:jyc46txjjba4rdewoqcmedyxlu

The Role of Long Noncoding RNAs in Gene Expression Regulation [chapter]

Zhijin Li, Weiling Zhao, Maode Wang, Xiaobo Zhou
2019 Gene Expression Profiling in Cancer [Working Title]  
Accumulating evidence highlights that noncoding RNAs, especially the long noncoding RNAs (lncRNAs), are critical regulators of gene expression in development, differentiation, and human diseases, such  ...  We also introduce the interaction between lncRNA and DNA, RNA and protein, and the bioinformatics applications on lncRNA research.  ...  Acknowledgements This work was partially supported by National Institutes of Health grants [NIH R01GM123037, U01AR069395-01A1, and U01CA166886] to X. Zhou.  ... 
doi:10.5772/intechopen.81773 fatcat:knjqnbtx4fes5nsacvwzt5474m

RStrucFam: a web server to associate structure and cognate RNA for RNA-binding proteins from sequence information

Pritha Ghosh, Oommen K. Mathew, Ramanathan Sowdhamini
2016 BMC Bioinformatics  
It will be useful to obtain an early understanding and association of RNA-binding property of sequences of gene products.  ...  RNA-binding proteins (RBPs) interact with their cognate RNA(s) to form large biomolecular assemblies.  ...  Declarations All authors have gone through the manuscript and contents of this article have not been published elsewhere.  ... 
doi:10.1186/s12859-016-1289-x pmid:27717309 pmcid:PMC5054549 fatcat:i6s4xeymlbfqnbpqtwpdkexiy4

Long Noncoding RNA Discovery in Cardiovascular Disease

Tamer Sallam, Jaspreet Sandhu, Peter Tontonoz
2018 Circulation Research  
The recent identification of a fascinating group of mediators known as long noncoding RNAs (lncRNAs) has provided a wealth of new biology to explore for cardiovascular risk mitigation. lncRNAs are expressed  ...  in a highly context-specific fashion, and multiple lines of evidence implicated them in diverse biological processes.  ...  Sources of Funding This work was supported by grants HL066088 and HL128822 from the National Heart, Lung, and Blood Institute.  ... 
doi:10.1161/circresaha.117.311802 pmid:29301847 pmcid:PMC5902384 fatcat:dkibfeg535bppgh3uhxxygoxy4

Long non-coding RNA LINC00672 contributes to p53 protein-mediated gene suppression and promotes endometrial cancer chemosensitivity

Wei Li, Hua Li, Liyuan Zhang, Min Hu, Fang Li, Jieqiong Deng, Mingxing An, Siqi Wu, Rui Ma, Jiachun Lu, Yifeng Zhou
2017 Journal of Biological Chemistry  
hnRNP K, guiding p53 binds to the p53RE of LASP1, forming a p53 regulation loop.  ...  3 The abbreviations used are: EC, endometrial carcinoma; lincRNA, long intergenic ncRNA; hnRNP, heterogeneous nuclear ribonucleoprotein; qRT, quantitative RT; RNAP, RNA polymerase; nt, nucleotide; LNA,  ...  Interestingly, the binding predictions showed that heterogeneous nuclear ribonucleoprotein F and H (hnRNP F and hnRNP H) bind precisely to the ϳ125-nt highly evolutionarily conserved sequence in the 5Ј-portion  ... 
doi:10.1074/jbc.m116.758508 pmid:28232485 pmcid:PMC5392574 fatcat:2xb2aazh7vddnpswsohpnvg4au

The Ever-Evolving Concept of the Gene: The Use of RNA/Protein Experimental Techniques to Understand Genome Functions

Andrea Cipriano, Monica Ballarino
2018 Frontiers in Molecular Biosciences  
LncRNAs display a dynamic pattern of expression in differentiation and development, the specific binding of transcription factors on their promoters, and the presence of peculiar chromatin signatures,  ...  The identification of binding sites can also be achieved by the use of alternative CLIP approaches, such as crosslinking and analysis of cDNA (CRAC) (Bohnsack et al., 2012) and the individual-nucleotide  ...  Copyright © 2018 Cipriano and Ballarino. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY).  ... 
doi:10.3389/fmolb.2018.00020 pmid:29560353 pmcid:PMC5845540 fatcat:6n4gs77f5vakhm2qb5vu52ydma

LncPRESS1 Is a p53-Regulated LncRNA that Safeguards Pluripotency by Disrupting SIRT6-Mediated De-acetylation of Histone H3K56

Abhinav K. Jain, Yuanxin Xi, Ryan McCarthy, Kendra Allton, Kadir C. Akdemir, Lalit R. Patel, Bruce Aronow, Chunru Lin, Wei Li, Liuqing Yang, Michelle C. Barton
2016 Molecular Cell  
Accession Numbers RNA-Seq expression data can be accessed at NCBI Gene Expression Omnibus (GEO) (http://www.ncbi.nlm.nih.gov/geo/) under accession no. GSE76023.  ...  Acknowledgments We thank Kaushik Thakkar for assistance with microscopy and members of our laboratory for helpful discussions.  ...  Schematic representation of our p53 and histone ChIP-Seq data (untreated or +RA) showed p53 binding increased at regulatory regions of p53-responsive lncRNAs (Fig. 3A , and Supplemental Fig S3 ).  ... 
doi:10.1016/j.molcel.2016.10.039 pmid:27912097 pmcid:PMC5137794 fatcat:rrgo7wapjrctrb2gu2dvm65abu

Neurodegeneration as an RNA disorder

Rory Johnson, Wendy Noble, Gian Gaetano Tartaglia, Noel J. Buckley
2012 Progress in Neurobiology  
Since the sequencing of the human genome, we have come to appreciate that the transcriptional output of the human genome is extremely rich in non-protein coding RNAs (ncRNAs).  ...  This heterogeneous class of transcripts is widely expressed in the nervous system, and is likely to play many crucial roles in the development and functioning of this organ.  ...  ) : (A) In agreement with experimental evidence, catRAPID predicts the binding site of FMRP at position 150-217.  ... 
doi:10.1016/j.pneurobio.2012.09.006 pmid:23063563 pmcid:PMC7116994 fatcat:k6dr4ciffjdj3hb3wpltwn4kzu
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