RESEARCH PAPER www.landesbioscience.com Mobile Genetic Elements e27755-1 Mobile Genetic Elements 3, e27755; November/December 2013; © 2013 Landes Bioscience RESEARCH PAPER Introduction MicroRNAs (miRs) are short (approximately 20 nucleotide) noncoding RNAs (ncRNAs) involved in the regulation of gene expression. 1 Functioning much like small interfering RNAs (siR- NAs), miRs bind to complimentary messenger RNA (mRNA) resulting in the repression of translation. 2,3 MiRs are initially transcribed in the nucleus as portions of larger precursor mol- ecules called pri-miRs. These initial transcripts are processed by Drosha to generate ~70 nucleotide stem loops (pre-miRs) that are exported into the cytosol where Dicer ultimately trims these dsRNA pre-miRs into functional single stranded miRs. 2,4 Following this, complementary sequence association between a miR and mRNA target leads to inhibited translation of the mRNA molecule. 2 To date, our principal obstacle to deciphering miR function has proven to be our inability to accurately predict miR asso- ciation with target mRNAs. This is principally the result of the capacity of miRs to associate with mRNAs bearing imperfect sequence complementarities. 5 Although accurately determining which mRNAs a miR targets has been an extremely active area of research, no universal model of target prediction has been widely adopted. Unlike siRNAs which associate with targets through perfect complementarity, miR association requires as little as seven complementary nucleotides. 6 Usually located at the 5′ end of a miR, these seven complementary nucleotides are known as “seeds” and their complement in target mRNAs are known as “seed matches.” 7 This complementarity between seeds and seed matches is the core requirement for the majority of currently utilized miR target prediction algorithms after which programs *Correspondence to: Glen M Borchert; Email: borchert@southalabama.edu Submitted: 12/05/2013; Revised: 01/03/2014; Accepted: 01/07/2014 Citation: Roberts JT, Cooper EA, Favreau CJ, Howell JS, Lane LG, Mills JE, Newman DC, Perry TJ, Russell ME, Wallace BM, et al. Continuing analysis of microRNA origins: Formation from transposable element insertions and noncoding RNA mutations. Mobile Genetic Elements 2014; 3:e27755; http://dx.doi.org/10.4161/ mge.27755 Continuing analysis of microRNA origins Formation from transposable element insertions and noncoding RNA mutations Justin T Roberts, Elvera A Cooper, Connor J Favreau, Jacob S Howell, Lee G Lane, James E Mills, Derrick C Newman, Tabitha J Perry, Meaghan E Russell, Brittany M Wallace, and Glen M Borchert* Department of Biological Sciences, University of South Alabama; Mobile, AL USA Keywords: LINE, microRNA, miR, miRNA, noncoding RNA, repetitive, retrotransposon, SINE, transposable, transposon Abbreviations: Ago, argonaute; bp, base pair; LINE, long interspersed repeated element; LTR, long terminal repeat; miR, microRNA; mRNA, messenger RNAs; ncRNA, noncoding RNA; nt, nucleotide; OrBId, origin based identification of microRNA targets algorithm; ORF, open reading frame; RISC, RNA-Induced Silencing Complex; RNAi, RNA interference; rRNA, ribosomal RNA; scaRNA, small Cajal body-specific RNA; SINE, short interspersed repeated elements; siRNA, small interfering RNA; snoRNA, small nucleolar RNA; snRNA, spliceosomal RNA; sRNA, short regulatory RNA; TE, transposable element; tmRNA, transfer messenger RNA; tRNA, transfer RNA; UTR, untranslated region MicroRNAs (miRs) are small noncoding RNAs that typically act as regulators of gene expression by base pairing with the 3′ UTR of messenger RNAs (mRNAs) and either repressing their translation or initiating degradation. As of this writ- ing over 24,500 distinct miRs have been identified, but the functions of the vast majority of these remain undescribed. This paper represents a summary of our in depth analysis of the genomic origins of miR loci, detailing the formation of 1,213 of the 7,321 recently identified miRs and thereby bringing the total number of miR loci with defined molecular origin to 3,605. Interestingly, our analyses also identify evidence for a second, novel mechanism of miR locus generation through describing the formation of 273 miR loci from mutations to other forms of noncoding RNAs. Importantly, several independent investigations of the genomic origins of miR loci have now supported the hypothesis that miR hairpins are formed by the adjacent genomic insertion of two complementary transposable elements (TEs) into opposing strands. While our results agree that subsequent transcription over such TE interfaces leads to the formation of the majority of functional miR loci, we now also find evidence suggesting that a subset of miR loci were actually formed by an alternative mechanism—point mutations in other structurally complex, noncoding RNAs (e.g., tRNAs and snoRNAs).