MicroRNA targets in Drosophila

Abstract

The emerging combinatorics of miRNA target sites in the 3' untranslated regions of messenger RNAs are reminiscent of transcriptional regulation in promoter regions of DNA, with both one-to-many and many-to-one relationships between regulator and target. Typically, more than one miRNA regulates one message, indicative of cooperative translational control. Conversely, one miRNA may have several target genes, reflecting target multiplicity. As a guide to focused experiments, we provide detailed online information about likely target genes and binding sites in their untranslated regions, organized by miRNA or by gene and ranked by likelihood of match. The target prediction algorithm is freely available and can be applied to whole genome sequences using identified miRNA sequences. AbstractBackground: The recent discoveries of microRNA (miRNA) genes and characterization of the first few target genes regulated by miRNAs in Caenorhabditis elegans and Drosophila melanogaster have set the stage for elucidation of a novel network of regulatory control. We present a computational method for wholegenome prediction of miRNA target genes. The method is validated using known examples. For each miRNA, target genes are selected on the basis of three properties: sequence complementarity using a position-weighted local alignment algorithm, free energies of RNA-RNA duplexes, and conservation of target sites in related genomes. Application to the D. melanogaster, Drosophila pseudoobscura and Anopheles gambiae genomes identifies several hundred target genes potentially regulated by one or more known miRNAs.

Characterization of Trichuris muris secreted proteins and extracellular vesicles provides new insights into host–parasite communication

“…Only miRNA sequences commonly identified in both replicates were included for further analyses. The interaction between miRNA and murine host genes was predicted using the miRanda algorithm 3.3a [37]. Input 3ʹUTR from the M. musculus GRCm38.p4 assembly was retrieved from the Ensembl database release 86 [38].…”

Drosophila microRNAs exhibit diverse spatial expression patterns during embryonic development

“…For example, neural-specific miRNAs and muscle-specific miRNAs identified in this study are likely to function in the development and͞or physiology of the nervous system and musculature, respectively. Integration of these expression data with computational predictions of miRNA targets (27,32,33) will drive hypothesis-based functional studies of these miRNAs.…”

Principles and effects of microRNA-mediated post-transcriptional gene regulation

“…Another function of the 3 0 region of a miRNA is to give specificity to the members of miRNA families that share identical seeds but they diverge in their 3 0 sequences (Brennecke et al, 2005). The recognition of the principles of miRNA targeting accelerated the development and improvement of a series of bio-computational approaches to predict miRNA targets in animals that produced a remarkably large number of putative miRNA-regulated transcripts further emphasizing the significance of miRNAs (Enright et al, 2003;Stark et al, 2003;Kiriakidou et al, 2004;Lewis et al, 2005;Lall et al, 2006).…”