Logotipo do repositório
 

Publicação:
CeRNAs in plants: Computational approaches and associated challenges for target mimic research

Carregando...
Imagem de Miniatura

Orientador

Coorientador

Pós-graduação

Curso de graduação

Título da Revista

ISSN da Revista

Título de Volume

Editor

Tipo

Artigo

Direito de acesso

Acesso abertoAcesso Aberto

Resumo

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.

Descrição

Palavras-chave

Bioinformatics, CeRNA, Computational method, Consensus ceRNA motif, Noncoding RNA, Target mimics

Idioma

Inglês

Como citar

Briefings in Bioinformatics, v. 19, n. 6, p. 1273-1289, 2017.

Itens relacionados

Coleções

Unidades

Departamentos

Cursos de graduação

Programas de pós-graduação