New human and mouse microRNA genes found by homology search

Abstract

Conservation of microRNAs (miRNAs) among species suggests that they bear conserved biological functions. However, sequencing of new miRNAs has not always been accompanied by a search for orthologues in other species. I report herein the results of a systematic search for interspecies orthologues of miRNA precursors, leading to the identification of 35 human and 45 mouse new putative miRNA genes. MicroRNA tracks were written to visualize miRNAs in human and mouse genomes on the UCSC Genome Browser. Based on their localization, miRNA precursors can be excised either from introns or exons of mRNAs. When intronic miRNAs are antisense to the apparent host gene, they appear to originate from ill‐characterized antisense transcription units. Exonic miRNAs are, in general, nonprotein‐coding, poorly conserved genes in sense orientation. In three cases, the excision of an miRNA from a protein‐coding mRNA might lead to the degradation of the rest of the transcript. Moreover, three new examples of miRNAs fully complementary to an mRNA are reported. Among these, miR135a might control the stability and/or translation of an alternative form of the glycerate kinase mRNA by RNA interference. I also discuss the presence of human miRNAs in introns of paralogous genes and in miRNA clusters.

A bioinformatics-based update on microRNAs and their targets in rainbow trout (Oncorhynchus mykiss)

“…However, miRNAs were expressed limiting to specific developmental stages and tissues, so the discovery of miRNAs obtained in few tissues will certainly miss lots of miRNAs expressed in other tissues or developmental stages. As a result, computational-based approaches through the homology search at the EST level were used to identity additional miRNAs, which were often missed by methods such as direct-cloning and sequencing (Brameier, 2010;Weber, 2005;Zhang et al, 2005). Here in this work, amongst the 196 identified miRNAs in rainbow trout, only 29 miRNAs have been reported in previous researches (Table S1) , 2010), and the remaining 167 miRNAs were newly identified rainbow trout miRNAs.…”

“…However, the capability of these methods to detect miRNAs is too low-throughput and random. Since most miRNAs are evolutionarily highly-conserved among animals and plants (Altuvia et al, 2005;Liu et al, 2008;Reinhart et al, 2002), it is a powerful approach to predict new miRNA homologues by comparative genomics based on previously known miRNA sequences (Weber, 2005;Zhang et al, 2005). And large numbers of miRNAs have been successfully identified through comparative genomic computational strategies in a wide range of animals and plants (Bonnet et al, 2004;Lim et al, 2003).…”

Ectopic expression of miR-126*, an intronic product of the vascular endothelial EGF-like 7 gene, regulates prostein translation and invasiveness of prostate cancer LNCaP cells

“…The product, pre-miRNA, exits from the nucleus and is further processed by the cytoplasmic RNase III-like enzyme, Dicer, to generate the final miRNA. Interestingly, at least two dozen miRNA sequences (in humans) map within specific introns of protein-coding 'host' genes [19][20][21][22]. Although many of them appear to be conserved across species, the biogenesis and role of such 'intronderived' (or 'intronic') miRNAs remains a mystery.…”

RNAs everywhere: genome‐wide annotation of structured RNAs

“…Similarly, blast can be used to find orthologous ncRNAs in closely related species, e.g. Weber, 2005). In most cases, however, this approach is limited by the relatively fast evolution of most ncRNAs.…”