Abstract
BackgroundMost studies on the origin and evolution of microRNA in the human genome have been focused on its relationship with repetitive elements and segmental duplications. However, duplication events at a smaller scale (<1 kb) could also contribute to microRNA expansion, as demonstrated in this study.ResultsUsing comparative genome analysis and bioinformatics methods, we found nine novel expanded microRNA families enriched in short duplicated sequences in the human genome. Furthermore, novel genomic regions were found to contain microRNA paralogs for microRNA families previously analyzed to be related to segmental duplications. We found that for microRNA families expanded in the human genome, 14 families are specific to the primate lineage, and nine are non-specific, respectively. Two microRNA families (hsa-mir-1233 and hsa-mir-622) appear to be further expanded in the human genome, and were confirmed by fluorescence in situ hybridization. These novel microRNA families expanded in the human genome were mostly embedded in or close to proteins with conserved functions. Furthermore, besides the Alu element, L1 elements could also contribute to the origination of microRNA paralog families.ConclusionsTogether, we found that small duplication events could also contribute to microRNA expansion, which could provide us novel insights on the evolution of human genome structure and function.
Highlights
Most studies on the origin and evolution of microRNA in the human genome have been focused on its relationship with repetitive elements and segmental duplications
We found that novel microRNA family expanded in the human genome are located close to proteins with conserved function, and confirmed two of the microRNA expansion events by fluorescence in situ hybridization
We focused on detecting microRNA paralogs enriched in short duplication events (
Summary
Novel expanded microRNA families in the human genome To explore the relationship between short duplicated genomic sequences and the expansion of certain microRNA families in the human genome, we used repeatmasked reference genome for pairwise comparison (see Methods), since microRNA associated with repetitive elements have been well characterized [16,17,18]. Since the number of microRNAs deposited in the public database are far less than predicted, new microRNA paralogs and clusters may still exist in the human genome This method can be extended for other noncoding RNAs, which can potentially reveal interesting patterns of specific important duplications in the human genome. While numerous molecular mechanisms could be hypothesized for microRNA expansion, there remains a strong association that specific repetitive elements may have played important roles in the evolution of microRNA containing loci in humans These duplicated paralogs could obtain partial and/or novel functions or exert dosage effects, acquire novel regulatory elements for tissue-specific expression, possess modifications in seed sequence resulting in novel microRNAs, and potentially beneficial or detrimental to certain individuals or a specific population [29]. Further detailed analysis on the association of microRNA expansion with features unique to each ethnic group will potentially reveal their biological importance in human diversity
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