Abstract
BackgroundMicroRNAs (miRNAs) are small noncoding RNAs (~22 nucleotides) that regulate gene expression by cleaving mRNAs or inhibiting translation. The baboon is a well-characterized cardiovascular disease model; however, no baboon miRNAs have been identified. Evidence indicates that the baboon and human genomes are highly conserved; based on this conservation, we hypothesized that comparative genomic methods could be used to identify baboon miRNAs.MethodsWe employed an in silico comparative genomics approach and human miRNA arrays to identify baboon expressed miRNAs in liver (n = 6) and lymphocytes (n = 6). Expression profiles for selected miRNAs in multiple tissues were validated by RT-PCR.ResultsWe identified in silico 555 putative baboon pre-miRNAs, of which 41% exhibited 100% identity and an additional 58% shared more than 90% sequence identity with human pre-miRNAs. Some of these miRNAs are primate-specific and are clustered in the baboon genome like human miRNA clusters. We detected expression of 494 miRNAs on the microarray and validated expression of selected miRNAs in baboon liver and lymphocytes by RT-PCR. We also observed miRNA expression in additional tissues relevant to dyslipidemia and atherosclerosis. Approximately half of the miRNAs expressed on the array were not predicted in silico suggesting that we have identified novel baboon miRNAs, which could not be predicted using the current draft of the baboon genome.ConclusionWe identified a subset of baboon miRNAs using a comparative genomic approach, identified additional baboon miRNAs using a human array and showed tissue-specific expression of baboon miRNAs. Our discovery of baboon miRNAs in liver and lymphocytes will provide resources for studies on the roles of miRNAs in dyslipidemia and atherosclerosis, and for translational studies.
Highlights
MicroRNAs are small noncoding RNAs (~22 nucleotides) that regulate gene expression by cleaving mRNAs or inhibiting translation
Information on the predicted baboon miRNAs including names, genomic coordinates, length, mismatches and percent identity with human premiRNA sequences are available in Additional file 2
Of the 555 predicted baboon miRNAs, 227 (40.9%) shared 100% sequence identity with the human pre-miRNAs and 319 (57.5%) had greater than 90% and less than 100% identity with human pre-miRNAs (Table 1)
Summary
MicroRNAs (miRNAs) are small noncoding RNAs (~22 nucleotides) that regulate gene expression by cleaving mRNAs or inhibiting translation. Guided by RISC, the miRNAs silence gene expression by degrading target mRNA when there is complete basepairing, or by inhibiting translation when there is imperfect binding to the 3' untranslated region (UTR) [8,9]. Recent studies indicate that the up-regulation of miR-335 and 122 is associated with lipid metabolism in obese mice [18,19]. This suggests that miRNA dysregulation may play a role in disease phenotypes and that miRNAs may be important biomarkers for disease diagnosis [20,21]
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