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Microrna Biogenesis and Variability

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Microrna Biogenesis and Variability DOI 10.1515/bmc-2013-0015 BioMol Concepts 2013; 4(4): 367–380 Review Jes ú s Garc í a-L ó pez , Miguel A. Brie ñ o-Enr í quez and Jes ú s del Mazo * MicroRNA biogenesis and variability Abstract: MicroRNAs (miRNAs) are cell-endogenous small through RNA interference. The interaction between noncoding RNAs that, through RNA interference, are miRNAs and their mRNA targets blocks the regular transla- involved in the posttranscriptional regulation of mRNAs. tion or induces the degradation of targeted mRNAs. Micro- The biogenesis and function of miRNAs entail multiple RNAs might regulate about 60% of mammalian coding elements with different alternative pathways. These con- genes and show specific profiles of expression at the level fer a high versatility of regulation and a high variability of cell types and developmental stages. Genes coding for to generate different miRNAs and hence possess a broad miRNAs are scattered throughout mammalian genomes potential to regulate gene expression. Here we review the in intragenic and intergenic positions. At present, 1600 different mechanisms, both canonical and noncanoni- miRNA precursor molecules, which generate 2042 mature cal, that generate miRNAs in animals. The ‘ miRNome ’ forms, have been identified in the human genome [accord- panorama enhances our knowledge regarding the fine ing to miRNA databases (miRBase) release 19] (2, 3) . Mouse regulation of gene expression and provides new insights and rat genomes encode 1281 and 723 mature miRNAs, concerning normal, as opposed to pathological, cell dif- respectively (2, 3) . However, it is possible that the exist- ferentiation and development. ing difference with respect to the size of the human and rodent ‘ miRNomes ’ results from a more exhaustive quest Keywords: canonical biogenesis; editing; microRNAs; for human miRNAs. In fact, miRNAs are well conserved in noncanonical biogenesis; isomiRs. eukaryotic organisms (4) and are thought to be the result of a vital and evolutionarily ancient component of genetic regulation. *Corresponding author: Jes ú s del Mazo, Department of Cellular The binding of mature miRNAs to their target mRNAs and Molecular Biology, Centro de Investigaciones Biol ó gicas (CIB), Consejo Superior de Investigaciones Cient í ficas (CSIC), Ramiro de occurs through a specific miRNA region of about 6 – 8 nt in Maeztu, 9, E-28040 Madrid, Spain, e-mail: [email protected] length. This region is termed the ‘ seed region ’ and allows Jes ú s Garc í a-L ó pez and Miguel A. Brie ñ o-Enr í quez: Department for each of these small RNAs to regulate the expression of Cellular and Molecular Biology, Centro de Investigaciones of hundreds of genes, generally by binding to the mRNA Biol ó gicas (CIB), Consejo Superior de Investigaciones Cient í ficas 3 ′ untranslated region (UTR). MicroRNAs that share a (CSIC), Ramiro de Maeztu, 9, E-28040 Madrid, Spain similar ‘ seed region ’ belong to the same miRNA family. In general, members of a miRNA family regulate related genes or are involved in the regulation of similar biologi- cal events. Several families of miRNAs in mammals have Introduction been described, some of which are related to mechanisms of differentiation and self-renewal and thus have been MicroRNAs (miRNAs) are small noncoding RNAs [ ≈ 21 – 23 suggested as possible biomarkers for these types of pro- nucleotides (nt)] that act through RNA interference as cesses. For example, the let-7 or miR-30 families promote posttranscriptional regulators of gene expression and differentiated cell fates, whereas miR-290 family members play important roles in many developmental and cellular are associated with self-renewal events. processes of eukaryotic organisms. Although the miRNA Although miRNAs are the best characterized small biogenesis pathways are similar in different phyla, there noncoding RNAs, some aspects of their biogenesis still exist some differences between plants and animals that remain to be uncovered. Recent studies (5 – 11) have revealed require a different study with respect to either biogenesis alternative mechanisms of biogenesis and recycling of pathway (1) . We will focus in this review on the biogenesis miRNAs. This review will mainly focus on the mecha- of the miRNAs associated with the animal kingdom. nisms of miRNA biogenesis generated by both canonical MicroRNAs negatively regulate gene expression via and noncanonical pathways. Furthermore, we will review base pairing with complementary mRNA sequences the miRNA recycling mechanisms and posttranscriptional 368 J. Garc í a-L ó pez et al.: MicroRNA biogenesis modifications due to the alternative processing of precur- bind to the different types of small noncoding interfer- sors and editing processes. Recycling mechanisms allow ence RNAs such as miRNAs, endogenous small inter- the production of new mature miRNA molecules without a fering RNAs (endo-siRNAs), and piwi-interacting RNAs need to generate new miRNA precursors. (piRNAs). In mammals, seven AGO family proteins have been described. These proteins have been classified in two subfamilies known as the AGO subfamily and the The canonical miRNA biogenesis PIWI subfamily (31 – 34) . The proteins encompassed in the AGO subfamily (AGO1 – 4) are involved in the miRNA pathway and the endo-siRNA pathways; nonetheless, only AGO2 displays endonuclease activity (35 – 37) . On the contrary, Typically, miRNA biogenesis is directed through a spe- PIWI proteins are only involved in the piRNA pathway. cific promoter or as part of a host gene in which miRNA is usually enclosed within intronic regions. Some miRNAs are closely located in a genome and are transcribed as The noncanonical biogenesis of part of a common transcript (cluster of miRNAs) similar to polycistronic units (12, 13) . RNA polymerase II transcribes miRNAs miRNA genes as large polyadenylated RNA molecules named primary miRNAs (pri-miRNAs) (14 – 16) ( Figure 1 ). In the past few years, alternative sources of miRNAs have These pri-miRNAs contain complementary sequence emerged. The biogenesis of such miRNAs entails some regions capable of materializing stem loops that include elements belonging to the canonical pathway, but the bulges and mismatches. Pri-miRNAs are processed in the genomic origin differs from that of the classical miRNAs nucleus by a protein complex containing the RNase III ( Figure 1 ). Although most miRNAs are located in intergenic enzyme double-stranded RNA-specific endoribonuclease regions, some are derived from intragenic segments. A nuclear type III (DROSHA, also known as RNASEN) and particular miRNA type derived from intratranscribed loci microprocessor complex subunit DiGeorge syndrome criti- is that known as mirtron, together with its variant called cal region 8 (DGCR8) (17, 18) . As a result of this processing, a sintrom. Mirtrons, localized in the intronic regions of pri-miRNAs are cleaved into smaller double-stranded RNA mRNAs, can generate double-stranded loop structures as (dsRNA) molecules known as pre-microRNAs. In mammals do the regular miRNAs but are processed to pre-miRNAs and other vertebrates, together with flies, pre-miRNAs are by the spliceosome machinery ( Figure 1 ). Their biogenesis exported to the cytoplasm by exportin 5 (XPO5) (19 – 21) . In pathway is DROSHA/DGCR8 independent as was demon- the cytoplasm, pre-microRNAs are cleaved and despoiled strated in Drosha mutants (38) and DGCR8 knockout cells of their loops by the RNase III enzyme cytoplasmic endori- (39, 40) . The existence of mirtrons, initially discovered in bonuclease with dsRNA ‘ dicing ’ activity (DICER), which, Caenorhabditis elegans and Drosophila melanogaster (41, through interaction with the protein TRBP, produces 42) , has been demonstrated in different organisms, from dsRNAs characterized by overhangs of 2 – 3 nt at both plants to mammals (43 – 45) . Following the resolution of ends (22, 23) . These processed products are known as the intron lariat, the RNA product of splicing adopts a miRNA duplexes, as functional mature miRNAs are single pre-miRNA-like form, which can be further processed as a stranded. The last processing step requires the active par- canonical pre-miRNA bound to XPO5 then be transferred ticipation of a ribonucleoprotein complex known as RNA- to the cytoplasm to continue with the canonical pathways induced silencing complex (RISC), which can unwind both ( Figure 1 ). The usual concept regarding a mirtron entails strands. Although either strand of the miRNA duplex could that the pre-miRNA-like mirtron is generated by the direct potentially act as a mature miRNA, usually only one of the cleavage and excision within the splice donor and accep- strands is incorporated into the RISC complex to induce tor sites of the mRNA. That is, the splisosome machinery mRNA silencing (24, 25) . The strand selection process generates both prime ends of the pre-mirtron. However, is still a subject of study full of recurrent controversies not in all pre-mirtrons do the ends of the double-stranded (24 – 29) . The specificity of either strand has been associ- regions coincide with the ends of the intron. Some pre- ated with different cell types and developmental stages mirtrons retain a single-stranded tail at the 3 ′ or 5 ′ end (30) . Once loaded, RISC mediates in the recognition of the (39, 41, 46) that has to be processed before proceeding mRNA to be targeted. to the cytoplasmic export and cleavage by DICER. Such The key components of the RISC complex are the trimming is carried out by the action of the RNA exosome Argonaute (AGO) family proteins
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