Comparative genomic analysis of upstream miRNA regulatory motifs in Caenorhabditis
| Autor: | Jeremy C. Gray, Richard Jovelin, Patrick C. Phillips, Aldis Krizus, Julie M. Claycomb, Bakhtiyar Taghizada, Asher D. Cutter |
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| Rok vydání: | 2015 |
| Předmět: |
0301 basic medicine
Comparative genomics Regulation of gene expression Computational biology Biology Regulatory Sequences Nucleic Acid Non-coding RNA biology.organism_classification Article Caenorhabditis 03 medical and health sciences MicroRNAs 030104 developmental biology Gene Expression Regulation Regulatory sequence Animals RNA Helminth Sequence motif Enhancer Molecular Biology Gene Phylogeny |
| Zdroj: | RNA (New York, N.Y.). 22(7) |
| ISSN: | 1469-9001 |
| Popis: | MicroRNAs (miRNAs) comprise a class of short noncoding RNA molecules that play diverse developmental and physiological roles by controlling mRNA abundance and protein output of the vast majority of transcripts. Despite the importance of miRNAs in regulating gene function, we still lack a complete understanding of how miRNAs themselves are transcriptionally regulated. To fill this gap, we predicted regulatory sequences by searching for abundant short motifs located upstream of miRNAs in eight species of Caenorhabditis nematodes. We identified three conserved motifs across the Caenorhabditis phylogeny that show clear signatures of purifying selection from comparative genomics, patterns of nucleotide changes in motifs of orthologous miRNAs, and correlation between motif incidence and miRNA expression. We then validated our predictions with transgenic green fluorescent protein reporters and site-directed mutagenesis for a subset of motifs located in an enhancer region upstream of let-7. We demonstrate that a CT-dinucleotide motif is sufficient for proper expression of GFP in the seam cells of adult C. elegans, and that two other motifs play incremental roles in combination with the CT-rich motif. Thus, functional tests of sequence motifs identified through analysis of molecular evolutionary signatures provide a powerful path for efficiently characterizing the transcriptional regulation of miRNA genes. |
| Databáze: | OpenAIRE |
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