CeRNAs in plants: Computational approaches and associated challenges for target mimic research
| Autor: | Irma Lozada-Chávez, Douglas Silva Domingues, Alexandre Rossi Paschoal, Peter F. Stadler |
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| Přispěvatelé: | UTFPR - CÂMPUS CORNELIO PROCOPIO, University Leipzig, University of Leipzig, Universidade Estadual Paulista (Unesp) |
| Jazyk: | angličtina |
| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Computer science Competing endogenous RNA Mechanism (biology) Bioinformatics Molecular Mimicry Computational Biology Computational biology Plants Computational method Genome Noncoding RNA 03 medical and health sciences MicroRNAs 030104 developmental biology RNA Plant Target mimics microRNA CeRNA Identification (biology) Experimental work Molecular Biology Function (biology) Information Systems Consensus ceRNA motif |
| Zdroj: | Scopus Repositório Institucional da UNESP Universidade Estadual Paulista (UNESP) instacron:UNESP |
| Popis: | Made available in DSpace on 2019-10-06T15:18:04Z (GMT). No. of bitstreams: 0 Previous issue date: 2017-05-30 Fondo Nacional de Desarrollo Científico y Tecnológico Consejo Nacional de Ciencia y Tecnología Deutscher Akademischer Austauschdienst The competing endogenous RNA hypothesis has gained increasing attention as a potential global regulatory mechanism of microRNAs (miRNAs), and as a powerful tool to predict the function of many noncoding RNAs, including miRNAs themselves. Most studies have been focused on animals, although target mimic (TMs) discovery as well as important computational and experimental advances has been developed in plants over the past decade. Thus, our contribution summarizes recent progresses in computational approaches for research of miRNA:TM interactions. We divided this article in three main contributions. First, a general overview of research on TMs in plants is presented with practical descriptions of the available literature, tools, data, databases and computational reports. Second, we describe a common protocol for the computational and experimental analyses of TM. Third, we provide a bioinformatics approach for the prediction of TM motifs potentially cross-targeting both members within the same or from different miRNA families, based on the identification of consensus miRNA-binding sites from known TMs across sequenced genomes, transcriptomes and known miRNAs. This computational approach is promising because, in contrast to animals, miRNA families in plants are large with identical or similar members, several of which are also highly conserved. From the three consensus TM motifs found with our approach: MIM166, MIM171 and MIM159/319, the last one has found strong support on the recent experimental work by Reichel and Millar [Specificity of plant microRNA TMs: cross-targeting of mir159 and mir319. J Plant Physiol 2015;180:45-8]. Finally, we stress the discussion on the major computational and associated experimental challenges that have to be faced in future ceRNA studies. UTFPR - CÂMPUS CORNELIO PROCOPIO, 1640 Avenue Alberto Carazzai Bioinformatics Group Department of Computer Science and Interdisciplinary Center for Bioinformatics University Leipzig, Härtelstraße 16-18 Interdisciplinary Center for Bioinformatics University of Leipzig Department of Botany Institute of Biosciences São Paulo State University (UNESP) Department of Botany Institute of Biosciences São Paulo State University (UNESP) Fondo Nacional de Desarrollo Científico y Tecnológico: 00454505/2014-0 Consejo Nacional de Ciencia y Tecnología: 185993 Deutscher Akademischer Austauschdienst: 57314018 |
| Databáze: | OpenAIRE |
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