Human miRNA Precursors with Box H/ACA snoRNA Features

Citation: Scott MS, Avolio F, Ono M, Lamond AI, Barton GJ ( Human miRNA Precursors with Box H/ACA snoRNA Features Ron Unger, Bar-Ilan University, Israel 0 1 Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Dundee , United Kingdom , 2 Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee , Dundee , United Kingdom MicroRNAs (miRNAs) and small nucleolar RNAs (snoRNAs) are two classes of small non-coding regulatory RNAs, which have been much investigated in recent years. While their respective functions in the cell are distinct, they share interesting genomic similarities, and recent sequencing projects have identified processed forms of snoRNAs that resemble miRNAs. Here, we investigate a possible evolutionary relationship between miRNAs and box H/ACA snoRNAs. A comparison of the genomic locations of reported miRNAs and snoRNAs reveals an overlap of specific members of these classes. To test the hypothesis that some miRNAs might have evolved from snoRNA encoding genomic regions, reported miRNA-encoding regions were scanned for the presence of box H/ACA snoRNA features. Twenty miRNA precursors show significant similarity to H/ACA snoRNAs as predicted by snoGPS. These include molecules predicted to target known ribosomal RNA pseudouridylation sites in vivo for which no guide snoRNA has yet been reported. The predicted folded structures of these twenty H/ACA snoRNA-like miRNA precursors reveal molecules which resemble the structures of known box H/ACA snoRNAs. The genomic regions surrounding these predicted snoRNA-like miRNAs are often similar to regions around snoRNA retroposons, including the presence of transposable elements, target site duplications and poly (A) tails. We further show that the precursors of five H/ACA snoRNA-like miRNAs (miR-151, miR-605, mir-664, miR-215 and miR-140) bind to dyskerin, a specific protein component of functional box H/ ACA small nucleolar ribonucleoprotein complexes suggesting that these molecules have retained some H/ACA snoRNA functionality. The detection of small RNA molecules that share features of miRNAs and snoRNAs suggest that these classes of RNA may have an evolutionary relationship. - Funding: MSS is a recipient of post-doctoral fellowships from the Canadian Institutes of Health Research (CIHR) as well as the Caledonian Research Foundation. Funding for this research was provided by a Wellcome Trust Programme to AIL (Ref: 073980/Z/03/Z). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. Small nucleolar RNAs (snoRNAs) and microRNAs (miRNAs) are two classes of abundant non-coding regulatory RNAs that carry out fundamental cellular activities but that have only been comprehensively investigated in recent years. SnoRNAs are small RNA molecules of approximately 60300 nucleotides in length which generally serve as guides for the catalytic modification of selected ribosomal RNA nucleotides [1,2]. SnoRNAs associate with specific proteins, which are conserved amongst all eukaryotes, to form small nucleolar ribonucleoparticles (snoRNPs). Two main groups of snoRNAs have been described. The box C/D snoRNAs, which bind the four conserved core box C/D snoRNP proteins fibrillarin, NOP56, NOP5/NOP58 and NHP2L1, are involved in 29-O-ribose methylation. The box H/ACA snoRNAs, which bind the four conserved core box H/ACA snoRNP proteins DKC1 (dyskerin), GAR1, NHP2 and NOP10, catalyse pseudouridylation. In vertebrates, most snoRNAs have been shown to reside in introns of protein coding host genes and are processed out of the excised introns [3]. However, two box C/D snoRNAs have recently been found to be transcribed from independent RNA pol II units [4]. MiRNAs are ,1824 nucleotide-long RNAs that are processed out of ,70 nucleotide-long hairpin structures (called pre-miRNAs) [5]. In mammals, miRNAs have been shown to be involved mainly in mRNA translation inhibition [6] although recently, they have also been reported to activate translation [7]. A large class of miRNAs are encoded in introns of protein-coding genes and are co-expressed with these host genes [810]. The remaining miRNAs are encoded in independent transcription units. Some of these miRNAs have been shown to be under the control of the RNA polymerase II [11] while others are transcribed by the RNA polymerase III [12]. Many members of the snoRNA and miRNA classes are well conserved throughout evolution [1,2,13]. Correspondence between several yeast and human snoRNAs and their target sites have been established and many snoRNAs have a very high sequence identity within mammals as shown in the snoRNAbase database [14]. In the case of miRNAs, several families have been found to be well conserved in metazoans [13,15]. However, recent reports also suggest the existence of species- and lineagespecific snoRNAs and miRNAs [13,16,17]. These and other reports on their origin and evolution are providing clues about the emergence of large groups of these recently evolved molecules. Through bioinformatic searches, Weber [17] and Luo and Li [16] identified hundreds of human snoRNAs and snoRNA-related molecules that are derived from transposable The major functions known for RNA were long believed to be either messenger RNAs, which function as intermediates between genes and proteins, or ribosomal RNAs and transfer RNAs which carry out the translation process. In recent years, however, newly discovered classes of small RNAs have been shown to play important cellular roles. These include microRNAs (miRNAs), which can regulate the production of specific proteins, and small nucleolar RNAs (snoRNAs), which recognise and chemically modify specific sequences in ribosomal RNA. Although miRNAs and snoRNAs are currently believed to be generated by different cellular pathways and to function in different cellular compartments, members of these two types of small RNAs display numerous genomic similarities, and a small number of snoRNAs have been shown to encode miRNAs in several organisms. Here we systematically investigate a possible evolutionary relationship between snoRNAs and miRNAs. Using computational analysis, we identify twenty genomic regions encoding miRNAs with highly significant similarity to snoRNAs, both on the level of their surrounding genomic context as well as their predicted folded structure. A subset of these miRNAs display functional snoRNA characteristics, strengthening the possibility that these miRNA molecules might have evolved from snoRNAs. elements (TEs), thus confirming the widespread nature of this phenomenon, initially described for a small number of snoRNAs [2,18]. These analyses suggest that many snoRNAs result from the retroposition of existing snoRNAs that used long interspersed nuclear element (LINE) machinery t (...truncated)