López-Valle ML, Shishkova S

Language: Spanish
References: 0
Page: 13-26
PDF size: 1007.05 Kb.

ABSTRACT

MicroRNAs (miRNAs) are small non-coding RNAs 20 to 24 nucleotides long that silence gene expression post-transcriptionally. De novo identification of miRNAs is based on features of its biogenesis. In general, the criteria considered are the identification on a transcript that folds into a stem-loop secondary structure, as well as the miRNA and miRNAs sequences resulting from small RNA-sequencing. These sequences should possess nearly perfect complementaritg, map onto the stem part of the secondary structure with a displacement of 2 nucleotides and represent most of the reads mapped onto the stemloop structure. In this article, the miRBase database, the conserved and lineage-specific miRNA with an emphasis on plant miRNAs, and the procedures of de novo identification of miRNAs based on prediction of the stem-loop structure are described. These bioinformatic methods employ data obtained by next generation sequencing techniques, that is, small RNA-seq, coupled witt RNA-seq for de novo transcriptome assembly, or available genome sequences. The methods of bioinformatic prediction and experimental validation of miRNA targets are also described.