Systematic analysis of human microRNA divergence based on evolutionary emergence

Abstract

a b s t r a c tMicroRNAs (miRNAs) play important roles in post-transcriptional gene expression control. To gain new insight into human miRNAs, we performed comprehensive sequence-based homology search for known human miRNAs to study the evolutionary distribution of human miRNAs. Furthermore, we carried out a series of studies to compare various features for different lineage-specific human miRNAs. Our results showed that major expansions of human miRNA genes coincide with the advent of vertebrates, mammals and primates. Further system-level analysis revealed significant differences in human miRNAs that arose from different evolutionary time points for a number of characteristics, implicating genetic and functional diversification for different human miRNAs during evolution. Our finds provide more useful knowledge for further exploring origins and evolution of human miRNA genes.

MicroRNA analysis in model species based on evolutionary rates

“…Only a small fraction of miRNAs have been located in the coding region of host genes (Berezikov et al, 2011). We found that fast-evolving miRNAs had the highest proportions of intragenic miRNAs, as found by Wang et al (2011), except in the zebrafish (Figure 4). Young or fast-evolving miRNAs preferred to be intragenic, which in turn suggests that introns might be a good location for the emergence of new miRNAs.…”

“…A novel miRNA could evolve from the following genomic sources: 1) gene duplications, including tandem duplications and non-local duplications; 2) introns (Isik et al, 2010); 3) transposable elements (Yuan et al, 2011); 4) pseudogenes, snoRNAs, and tRNAs (Pederson, 2010); 5) antisense miRNA transcripts; and 6) de novo emergence (Liu et al, 2008). miRNAs with high evolutionary rates are mostly young, reside in introns, are expressed at low levels, and seem species-specific (Wang et al, 2011;Guerra-Assunção and Enright, 2012;Zhu et al, 2012). In humans, miRNAs with low expression levels have high evolutionary rates (Liang and Li, 2009).…”

Cardiovascular RNA Interference Therapy

“…This revolutionary insight has triggered extensive research into the functions of the noncoding genome and also led to an extended theory of evolution. 11 Certain very ancient ncRNA systems are well conserved, 12 whereas others have diversified during evolution [13][14][15][16][17][18][19][20] ( Figure 1). The evolution of miRs has already been traced, allowing to distinguish ancient from recent miR families.…”

Untitled

“…MicroRNAs are small non-coding endogenous RNA evolutionarily conserved and consist of [18][19][20][21][22] nucleotides [1,2,3]. Functionally these are regulatory molecules and they negatively regulate the target mRNA post-transcriptionally by binding partial complementarity in 3'UTR leading to mRNA degradation and/or target translation inhibition.…”

“…Studies on miRNA phylogenetic conservation and its functional diversity suggest that miRNAs play important roles in evolution, by driving phenotypic variation during development [17]. Primate miRNAs have a complex evolutionary history characterized by the deep conservation of some miRNA and frequent gain or loss of miRNA during evolution [18,19].…”