MicroRNA biogenesis and variability

Jesús García-López; Miguel A. Brieño-Enríquez; Jesús del Mazo

doi:10.1515/bmc-2013-0015

Article Open Access

MicroRNA biogenesis and variability

Jesús García-López
Jesus García-López holds a PhD from Complutense University of Madrid. At present he is doing postdoctoral research at the Laboratory of Molecular Biology of Gametogenesis CIB-CSIC, Madrid, Spain. He has previously worked on the RNA interference pathways and he is involved in the study of this small RNAs as biomarkers for embryo viability.
, Miguel A. Brieño-Enríquez
Miguel A. Brieño-Enriquez, received his medical degree from Autonomous University of San Luis Potosi, Mexico, and his PhD from Autonomous University of Barcelona, Spain. His research includes the effects of endocrine disrupting chemicals on human fetal oocytes. At present, he is doing his postdoctoral research working on small RNAs and gonadal development at the Laboratory of Molecular Biology of Gametogenesis CIB-CSIC, Madrid, Spain.
and Jesús del Mazo
Jesús del Mazo, PhD, is the Scientific Research and Group Leader of the ‘Molecular Biology of Gametogenesis’ Laboratory at Centre for Biological Research, CSIC, Madrid, Spain. From 1987 to 1989 he was an Associate Researcher at the California Institute of Technology, Pasadena, USA, and in 2006 he was an Honory Professor at Universidad de Valparaíso, Chile. He is the author of more than 60 articles in the field of Molecular Biology and Genetics of germ cells in mammals.

Published/Copyright: August 2, 2013

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From the journal BioMolecular Concepts Volume 4 Issue 4

Abstract

MicroRNAs (miRNAs) are cell-endogenous small noncoding RNAs that, through RNA interference, are involved in the posttranscriptional regulation of mRNAs. The biogenesis and function of miRNAs entail multiple elements with different alternative pathways. These confer a high versatility of regulation and a high variability to generate different miRNAs and hence possess a broad potential to regulate gene expression. Here we review the different mechanisms, both canonical and noncanonical, that generate miRNAs in animals. The ‘miRNome’ panorama enhances our knowledge regarding the fine regulation of gene expression and provides new insights concerning normal, as opposed to pathological, cell differentiation and development.

Keywords: canonical biogenesis; editing; microRNAs; noncanonical biogenesis; isomiRs

Introduction

MicroRNAs (miRNAs) are small noncoding RNAs [≈21–23 nucleotides (nt)] that act through RNA interference as posttranscriptional regulators of gene expression and play important roles in many developmental and cellular processes of eukaryotic organisms. Although the miRNA biogenesis pathways are similar in different phyla, there exist some differences between plants and animals that require a different study with respect to either biogenesis pathway (1). We will focus in this review on the biogenesis of the miRNAs associated with the animal kingdom.

MicroRNAs negatively regulate gene expression via base pairing with complementary mRNA sequences through RNA interference. The interaction between miRNAs and their mRNA targets blocks the regular translation or induces the degradation of targeted mRNAs. MicroRNAs might regulate about 60% of mammalian coding genes and show specific profiles of expression at the level of cell types and developmental stages. Genes coding for miRNAs are scattered throughout mammalian genomes in intragenic and intergenic positions. At present, 1600 miRNA precursor molecules, which generate 2042 mature forms, have been identified in the human genome [according to miRNA databases (miRBase) release 19] (2, 3). Mouse and rat genomes encode 1281 and 723 mature miRNAs, respectively (2, 3). However, it is possible that the existing difference with respect to the size of the human and rodent ‘miRNomes’ results from a more exhaustive quest for human miRNAs. In fact, miRNAs are well conserved in eukaryotic organisms (4) and are thought to be the result of a vital and evolutionarily ancient component of genetic regulation.

The binding of mature miRNAs to their target mRNAs occurs through a specific miRNA region of about 6–8 nt in length. This region is termed the ‘seed region’ and allows for each of these small RNAs to regulate the expression of hundreds of genes, generally by binding to the mRNA 3′ untranslated region (UTR). MicroRNAs that share a 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 biological events. Several families of miRNAs in mammals have been described, some of which are related to mechanisms of differentiation and self-renewal and thus have been suggested as possible biomarkers for these types of processes. For example, the let-7 or miR-30 families promote differentiated cell fates, whereas miR-290 family members are associated with self-renewal events.

Although miRNAs are the best characterized small noncoding RNAs, some aspects of their biogenesis still remain to be uncovered. Recent studies (5–11) have revealed alternative mechanisms of biogenesis and recycling of miRNAs. This review will mainly focus on the mechanisms of miRNA biogenesis generated by both canonical and noncanonical pathways. Furthermore, we will review the miRNA recycling mechanisms and posttranscriptional modifications due to the alternative processing of precursors and editing processes. Recycling mechanisms allow the production of new mature miRNA molecules without a need to generate new miRNA precursors.

The canonical miRNA biogenesis pathway

Typically, miRNA biogenesis is directed through a specific 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 part of a common transcript (cluster of miRNAs) similar to polycistronic units (12, 13). RNA polymerase II transcribes miRNA genes as large polyadenylated RNA molecules named primary miRNAs (pri-miRNAs) (14–16) (Figure 1). These pri-miRNAs contain complementary sequence regions capable of materializing stem loops that include bulges and mismatches. Pri-miRNAs are processed in the nucleus by a protein complex containing the RNase III enzyme double-stranded RNA-specific endoribonuclease nuclear type III (DROSHA, also known as RNASEN) and microprocessor complex subunit DiGeorge syndrome critical region 8 (DGCR8) (17, 18). As a result of this processing, pri-miRNAs are cleaved into smaller double-stranded RNA (dsRNA) molecules known as pre-microRNAs. In mammals and other vertebrates, together with flies, pre-miRNAs are exported to the cytoplasm by exportin 5 (XPO5) (19–21). In the cytoplasm, pre-microRNAs are cleaved and despoiled of their loops by the RNase III enzyme cytoplasmic endoribonuclease with dsRNA ‘dicing’ activity (DICER), which, through interaction with the protein TRBP, produces dsRNAs characterized by overhangs of 2–3 nt at both ends (22, 23). These processed products are known as miRNA duplexes, as functional mature miRNAs are single stranded. The last processing step requires the active participation of a ribonucleoprotein complex known as RNA-induced silencing complex (RISC), which can unwind both strands. Although either strand of the miRNA duplex could potentially act as a mature miRNA, usually only one of the strands is incorporated into the RISC complex to induce mRNA silencing (24, 25). The strand selection process is still a subject of study full of recurrent controversies (24–29). The specificity of either strand has been associated with different cell types and developmental stages (30). Once loaded, RISC mediates in the recognition of the mRNA to be targeted.

Figure 1

MicroRNA biogenesis, degradation, storage, and recycling.

The figure illustrates the different pathways to generate functional miRNAs.

The key components of the RISC complex are the Argonaute (AGO) family proteins (31–34). AGO proteins bind to the different types of small noncoding interference RNAs such as miRNAs, endogenous small interfering RNAs (endo-siRNAs), and piwi-interacting RNAs (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 PIWI subfamily (31–34). The proteins encompassed in the AGO subfamily (AGO1–4) are involved in the miRNA and the endo-siRNA pathways; nonetheless, only AGO2 displays endonuclease activity (35–37). On the contrary, PIWI proteins are only involved in the piRNA pathway.

The noncanonical biogenesis of miRNAs

In the past few years, alternative sources of miRNAs have emerged. The biogenesis of such miRNAs entails some elements belonging to the canonical pathway, but the genomic origin differs from that of the classical miRNAs (Figure 1). Although most miRNAs are located in intergenic regions, some are derived from intragenic segments. A particular miRNA type derived from intratranscribed loci is that known as mirtron, together with its variant called a sintrom. Mirtrons, localized in the intronic regions of mRNAs, can generate double-stranded loop structures as do the regular miRNAs but are processed to pre-miRNAs by the spliceosome machinery (Figure 1). Their biogenesis pathway is DROSHA/DGCR8 independent as was demonstrated in Drosha mutants (38) and DGCR8 knockout cells (39, 40). The existence of mirtrons, initially discovered in Caenorhabditis elegans and Drosophila melanogaster (41, 42), has been demonstrated in different organisms, from plants to mammals (43–45). Following the resolution of the intron lariat, the RNA product of splicing adopts a pre-miRNA-like form, which can be further processed as a canonical pre-miRNA bound to XPO5 then be transferred to the cytoplasm to continue with the canonical pathways (Figure 1). The usual concept regarding a mirtron entails that the pre-miRNA-like mirtron is generated by the direct cleavage and excision within the splice donor and acceptor sites of the mRNA. That is, the splisosome machinery generates both prime ends of the pre-mirtron. However, not in all pre-mirtrons do the ends of the double-stranded regions coincide with the ends of the intron. Some pre-mirtrons retain a single-stranded tail at the 3′ or 5′ end (39, 41, 46) that has to be processed before proceeding to the cytoplasmic export and cleavage by DICER. Such trimming is carried out by the action of the RNA exosome components, such as the Rrp6 nuclear exonuclease at the 3′ tail, which stops its action at the secondary structure of the double-stranded stem of the pre-mirtron (46). In vertebrates, 5′-end-tailed mirtrons have been identified (39, 47, 48), whereas 3′-tailed pre-mirtrons have only been detected in Drosophila. Specific exonuclease trimming of the 5′-end-tailed pre-mirtrons has not been identified yet. Identification by deep sequencing of mirtrons in mammals (44) and the differences detected from those found in insects suggest a relatively late evolutionary diversification of mirtrons.

Recently discovered mirtron variants are the splicing-independent mirtron-like miRNAs, termed simtrons (49). The main characteristics of this new variant of noncanonical miRNA biogenesis are the spliceosome-independent but DROSHA-dependent processing of the pre-simtrons together with an XPO5 lack of dependence for transport to the cytoplasm. Replacement of DICER processing by AGO2 slicing of miRNAs was reported as a noncanonical alternative to the miRNA biogenesis of particular miRNA (36, 50–52). However, simtron processing is independent of DICER or AGO2. This novel type of mirtron-like microRNA enhances the mechanisms that control the regulation of miRNA biogenesis, and as a consequence, the functional role of specific miRNA originated from such alternative mechanisms.

Other sources of miRNAs bypassing canonical biogenesis have also been described. Some small nucleolar RNAs can render miRNAs (53, 54), which are similar to mirtrons substrates for processing in a DICER-dependent and DROSHA/DGCR-independent pathway (55). Transfer RNAs can also generate miRNAs that have to be sliced by DICER (56). We have also recently identified some piRNAs in oocyte and sperm mouse cells with potential mRNA targets, in other words, with functional roles similar to miRNAs (García-López J, Hourcade J, Alonso L, Cárdenas DB, del Mazo J, Characterization and parental contribution of piRNAs and endo-siRNAs to mouse zygotes, unpublished data).

Regulatory mechanisms involved in the miRNA biogenesis pathway

The main regulatory mechanisms that operate in the canonical miRNA biogenesis pathway act on three levels: first, during the transcription of pri-microRNAs; second, by means of the editing mechanisms that can disrupt the processing of precursors; finally, through the regulation of the processing machineries such as the DROSHA/DGCR8 complex or DICER.

With regard to the pri-microRNA regulation of transcription, in a manner similar to that of coding genes, it is mediated by transcription factors that are specific to cell types, respond to environmental stimuli, or are necessary to trigger developmental pathways. For example, transcription factors OCT4 and SOX2, which are involved in stem cell maintenance, in turn regulate the transcription of the mmu-miR-302 miRNA cluster (57–59). Both OCT4 and SOX2 proteins bind to the conserved promoter region of miR-302 in a manner that miR-302 and their cluster partners are expressed in the same cells or tissues and at the same time as Oct4 and Sox2 (60–62). Another example is the regulation of pri-miRNA-34 transcription by the P53 protein (63, 64). In response to DNA damage, P53 is activated and acts on the promoter of miR-34, thus activating expression. It is thought that miR-34 induces the stop signals of the cell cycle pathway. Additionally, similar to protein-coding genes, the methylation of promoter regions can affect miRNA expression. For example, miRNAs involved in tumor suppression such as miR-148, miR-34b/c, or miR-9 undergo aberrant hypermethylation patterns that have been associated with cancer (65–67). The fact that the methylation of regulatory genome regions can also operate on the regulation of miRNA expression implies that the epigenetic modifications of the genome at miRNA loci can induce additional checkpoints with reference to epigenome regulatory mechanisms.

Precursor miRNAs (pre-RNAs) can suffer sequence modifications by ‘editing’ before they are processed. The elicitors of the editing mechanisms are the protein family of the adenosine deaminases acting on RNA (ADAR) (68–71). The members of this family act on dsRNAs, including miRNAs, by modifying their nucleotide sequences. The editing process involves the specific deamination of one or more adenosine nucleotides by transforming adenosine into inosine (Figures 1 and 2) (68–71). Inosine is recognized by the translation machinery and in the RNA-RNA binding as nucleotide guanosine. However, it has been reported that editing can disrupt the recognition of pri- and pre-miRNA through the DROSHA/DGCR8 and DICER processing machineries (72, 73). Alternatively, when editing affects the seed sequence of mature miRNA, it can cause a phenomenon known as retargeting (74, 75). The editing mechanism will be discussed in detail later.

Figure 2

Schematic representation of the different types of possible modifications to generate variations with respect to a hypothetical canonical sequence (22 nt).

Finally, the activity of DROSHA/DGCR8 and DICER can be regulated during the biogenesis of some miRNAs. For example, the ribonucleoprotein hnRNPA1 binds to the loop region of pri-microRNA-18a to facilitate its processing by DROSHA/DGCR8 well ahead of their miRNA cluster partners (miR-17-92 cluster) (76, 77). Meanwhile, the activation of the ERK protein mediates the phosphorylation of TRBP by stabilizing the binding of pre-microRNAs with DICER (78). As a result of this phosphorylation, the precursor molecule processing efficiencies are increased. Another example is the regulation of the let-7 biogenesis. The protein LIN28 represses both the processing of pri-microRNA to pre-microRNA of the let-7 microRNA as well as the pre-microRNA-let-7 processing by DICER (79–81). Through a feedback mechanism, let-7 also regulates the translation of Lin28 mRNA (82).

Bioavailability and miRNA recycling

The global bioavailability of miRNAs is presumably related to the availability of the different elements of the miRNA biogenesis machinery. Changes in the levels of expression of the genes encoding for the biogenesis and function of miRNAs can be modulated during development or cell type differentiation (83). Key element depletion in the biogenesis pathway could condition the stop in production of new mature miRNAs. Such switch-off mechanisms can comprise functional roles during cell differentiation and development, which drive the reprogramming of the miRNA-mediated gene expression. For example, the suppression of the maternal program to initiate the zygotic activation program is one of the biological processes that occur during the early stages of embryo development after fertilization. The suppression of the miRNA activity during these stages in mammals was suggested by studies in Dgcr8^-/- mutant mice. Following this line, we have also reported on the global decay of expression of genes involved in the canonical biogenesis pathway from fertilization to blastocyst mouse embryos (5). However, a global lack of new miRNA biogenesis does not necessarily imply an absence of specific miRNA availability. We have previously demonstrated that in early embryo stages in which the expression of genes encoding proteins involved in the biogenesis of miRNAs was dramatically downregulated, specific miRNAs such as mmu-miR-292-3p and mmu-miR-292-5p could be preserved as double-stranded molecules through the ‘protection’ from the binding to mRNA targets, pseudogenes, duplex passenger strands, or other types of RNA-specific reservoirs (5) (Figure 1). A similar miRNA protection by their heteroduplex cognate mRNA targets has also been reported in C. elegans (84). Recent articles corroborate on the existence of such mature miRNA reservoirs in cells (7, 8, 85). These reservoirs have the capacity to capture mature miRNA molecules to inhibit the miRNA silencing activities (Figure 1). Some of these reservoirs are in fact RNA molecules that have a circular shape and can act as miRNA ‘sponges’ in which the miRNAs could be stored until their hypothetical recycling (6). This new type of RNA molecule has been termed circular RNAs (circRNAs) (7, 8).

The functional bioavailability of specific miRNAs can also be modulated by the regulation of endogenous elements able to ‘sequester’ miRNA molecules. This hypothesis has been demonstrated by the regulated expression of pseudogenes that share the 3′ UTR of their corresponding coding genes, allowing the binding of miRNAs that are naturally involved in the posttranscriptional negative regulation of the coding genes. This fact has been reported in the upregulation of PTEN caused by the over expression of PTENP1, a known PTEN pseudogene, resulting in the suppression of cell growth. In turn, PTEN mRNA can act as a decoy for miRNAs that would downregulate PTENP1 transcripts (86).

An as yet poorly characterized aspect of miRNA activity is the fate of these small RNA molecules after eliciting the mRNA silencing. Furthermore, how the miRNA-induced suppression finalizes still remains an enigma. MicroRNAs have an unexpectedly long half-life and can reach high cell concentrations (9), even when key miRNA biogenesis elements such as DROSHA/DGCR8 or DICER are absent (87) or show very low expression levels (5). The existence of miRNA recycling pathways following the regulation of their targets facilitates their turnover.

One of the main features of miRNAs is their capacity to regulate multiple mRNA targets. However, the number of target transcripts in a cell often exceeds the number of miRNAs capable of regulating their transcripts (88). It remains extremely difficult to explain how a relatively low number of miRNAs can downregulate a high number of transcripts. The constant recycling of miRNAs derived from loci where mRNA target degradation is being actively carried out could explain the efficiency of miRNAs with regard to their gene silencing activities. Recycling exponentially increases the capacity of each mature miRNA molecule to regulate even hundreds of mRNA molecules without requiring a new processing of the miRNA precursor molecule. Nevertheless, where and how these miRNAs are stored until use remains poorly understood. The existence of molecular miRNA reservoirs, as mentioned above, could explain some of the peculiarities of the functional miRNA dynamics. Before the discovery of circRNAs, the possibility that mRNA targets could act as active reservoirs of the miRNAs that regulate them had already been suggested (5).

In general, recent data have suggested that the interaction between miRNAs and their mRNA targets could be driven by dynamic ways. If the miRNA/mRNA interaction is the cause of target degradation, the miRNA could bind again to another, similar or different, mRNA target molecule. Nonetheless, if the binding between the miRNA and its target inhibits translation without an mRNA cleavage, then the miRNA could keep being attached to the mRNA target and the mRNA would act as a reservoir of miRNAs. Finally, other types of RNAs such as pseudogene-coded mRNAs or circRNAs could capture itinerant miRNAs, thus avoiding the interaction between miRNAs and their potential mRNA targets, which, in response to demand, could directly provide many functional and mature miRNAs.

‘One for all and all for one’: enhancing versatility

Based on the principles of miRNA-target recognition, on average, each miRNA can recognize about 100–200 potential target sites of the transcriptome (89–91), considering only the seed region of the miRNAs and the 3′ UTRs of the mRNAs, although additional interaction sites occur (92). In turn, each transcript has various predicted and functional miRNA sites (89, 93, 94). More than 50% of the human protein-coding genes contain conserved miRNA targeting sites (95). This implies that the number of combinatorial miRNA-mRNA interactions enormously enhance regulatory possibilities. Moreover, this potential variability is further expanded if we consider the alternative transcription of genes coding for mRNA targets [such as single-nucleotide polymorphism (SNPs), alternative polyadenylation sites, and alternative splicing products) along with all the different alternative modifications that result from the miRNA alternative biogenesis mechanisms.

MicroRNA editing

As dsRNAs, miRNA precursor molecules are targets of ADAR proteins. Recent evidence indicates that A-to-I editing of miRNA precursors (pri- and pre-miRNAs) affects both the miRNA function and biogenesis (96–98). The editing of miRNA precursor molecules can alter the DROSHA/DGCR8 and DICER/TRBP recognition and processing. Initially, evidence on miRNA editing was first observed during the processing of miR-22 (99) and was later also detected during the biogenesis of other miRNAs. Although, in the beginning, it was suggested that miRNA precursor editing acted as a negative modulator of miRNA biogenesis, it has recently been demonstrated that the edited mature miRNAs can coexist with canonic mature miRNA molecules in the cell (73, 74, 100). Actually, it has not been well established how the editing mechanisms trigger the elimination of miRNAs via Tudor staphylococcal nuclease (TUDOR) (97, 101) or, alternatively, modify miRNA precursors by changing their nucleotide sequence to generate the alternative mature miRNA isoforms (74). It seems that both routes act simultaneously. For example, research on miRNAs by deep sequencing in oocytes and zygotes revealed that mature miRNAs such as miR-376a, let7-g, miR-27a, and miR-411 contained a considerable number of A-to-I sequence editing. In contrast, the editing levels of other miRNAs, for instance, miR-151, miR-379, or miR-376b (-5p form), were low (74).

In general, the outcome of ADAR editing varies according to where the edited nucleotides are located. It has been established that the editing can impinge on the processing by DROSHA/DGCR8 and DICER/TRBP (98, 101). However, is not yet clear whether editing results in a change of any recognition sequence into miRNA precursor molecules or if, on the contrary, the spatial conformation of miRNA molecules is changed. As dsRNA molecules, the pri- and pre-microRNA adopt tridimensional structures that could determine the accessibility of proteins involved in miRNA biogenesis. Secondary structures are also determined by the nucleotide sequence. In this manner, A-to-I editing can modify the secondary structure of precursor molecules, hampering DROSHA/DGCR8 and DICER/TRBP recognition and in consequence hindering miRNA precursor processing.

The fate of the edited precursor molecules that are not processed has not been firmly established so far. Hypothetically, edited miRNA precursors could be maintained in cell reservoirs until needed for use, as occurs in mature miRNAs. Nevertheless, the degradation of the edited nonprocessed miRNA precursor molecules is the only mode reported so far (102). For example, the editing of miR-142 precursor molecules blocks the DROSHA/DGCR8 pri-microRNA cleavage (98). It has been observed that pri-miRNA-142 sequences displayed multiple A-to-I changes. These hyperedited miRNA precursors were degraded via TUDOR-SN. This endonuclease recognizes inosine residues in dsRNAs and induces their cleavage (98, 101, 102). Consequently, ADAR proteins could mark the miRNA precursor molecules that must be cleaved by hyperediting their adenosines. It has not been well established how many A-to-I changes are necessary to promote the degradation of pre-RNA molecules by TUDOR-SN. However, it was recently suggested that this degradation could occur for specific cytoplasm domains that have been named T-bodies (TUDOR-SN bodies) (74).

Nevertheless, editing can also modify the mature sequence of miRNAs. Such editing probably alters the function instead of the miRNA biogenesis. Due to the precise recognition requirement between the miRNA seed region and its specific target, A-to-I editing, which affects the seed region, can generate miRNA retargeting. However, in both mice and humans, editing and other polymorphisms are not promiscuously detected in the seed regions (74, 103), suggesting a strong selective constraint on the miRNA/mRNA recognition site. Finally, ADAR proteins can act directly on mRNAs by modifying the recognition site where the miRNAs potentially bind (104). This could also have an effect on the binding between the miRNA and their targets with regard to mRNA.

IsomiRs

Usually, miRNAs are annotated as a single defined sequence (105). Using RNA sequencing, it has been observed that a pre-miRNA often gives rise to more than one mature miRNA sequence (105–107). These variants are named isomiRs and almost all of these molecules were initially considered to be artifacts (105, 108–110). Currently, the capacity of isomiRs to be associated with RISC and the translational machinery of polysomes has been demonstrated, further indicating that they could also interact with mRNAs (108, 111). These miRNA variants can encompass substitutions, insertions, or deletions (polymorphic isomiRs), 3′-isomiRs, and 5′-isomiRs. 5′- and 3′-isomiRs include nontemplate additions and 5′-3′ cleavage variations (105, 108) (Figure 2).

In terms of the number of miRNAs and their overall abundance, the most common type of isomiR in animals and plants consist of the 3′ isomiRs (111–114). As in regular miRNAs, isomiRs vary among different cells or tissues and according to specific biological stimuli (112–115). This suggests that the presence of some isomiRs could be regulated according to different cell functions.

5′ and 3′ Template modifications

It has been assumed that DICER needs a defined pre-miRNA distance of 22 nt from the 5′ to the 3′ end to be able to cleave both strands to produce a miRNA duplex (116–119). However, a high proportion of the identified isomiRs containing 5′ and 3′ modifications were derived from processing variations in the cleavage position of the precursor molecules by the DROSHA or DICER enzymes (105, 120, 121). The most abundant isomiRs have been found to differ only by 1 or 2 nt at the 5′ or 3′ end of their sequences (121). These results have indicated that DROSHA is more specific than DICER during the cleavage process. Consequently, more variations with regard to cleavage sites occur near the loop as compared with the base of the stem in pre-miRNA hairpins. DICER’s cleavage imprecision can be explained by the simultaneous DICER protein recognition of the RNA recognition protein domain and the RNAse III domain. DICER’s dual recognition permits to adopt a relatively flexible structure that accommodates pre-miRNA substrates, whereas the RNA recognition associated with DROSHA cleavage is provided only by protein DGCR8 (122, 123).

Changes in miRNA templates could also be associated with exoribonucleases. MicroRNAs bound to AGO proteins could be modified by nucleolytic trimming at the 3′ ends to generate isomiRs. For example, in the Drosophila miRNA biogenesis pathway, Liu et al. (124) found that mir-34 displays multiple isoforms that differ at the 3′ end. These isoforms are produced by the action of the 3′→5′ exoribonuclease CG9247/NIBBLER. Trimming of miRNA at the 3′ ends occurs after the removal of the passenger miRNA strand from the pre-RISC and may be the final step of the RISC assembly, ultimately enhancing the target (125).

5′ and 3′ Nontemplate modifications

The 3′ ends of mature miRNAs are highly heterogeneous, whereas the 5′ ends, which correspond to the seed regions, are relatively invariable. The patterns and sources of heterogeneity seem to vary depending on the miRNA species and according to the cell type. The 3′ ends often contain one to three extra nucleotides that do not match with the genomic DNA sequences. Sequence alterations of miRNAs can occur by the addition of nontemplate nucleotides to the miRNA termini (109, 126). The first description of a 3′-end modification of small RNA was rendered in the hen1 mutant of Arabidopsis (127). HEN1 is a methyl transferase that adds a methyl group to the 2′-OH at the 3′ end of the RNA (128). The addition of nucleotides is performed by a group of nucleotidyl transferases (129). In humans, there are 12 nucleotidyl transferases, seven of which are implicated in isomiR generation [reviewed by Neilsen et al. (105)]. In both humans and mice, these enzymes have uridyltranferase and/or adenyltransferase activity, which explain the most frequent nontemplate modifications such as insertions of single or multiple U (uridylation) or A (adenylation) (130). Uridylation plays a significant role in the control of miRNA biogenesis. In mammalian embryonic stem cells, let-7 biogenesis is suppressed by the LIN28 protein, which binds to the terminal loop of let-7 precursors (131, 132). Of special interest is the fact that LIN28 induces the 3′ uridylation of pre-let-7 by recruiting the terminal nucleotidyl transferase TUT4 (133). The oligo U-tail added by TUT4 blocks the DICER processing mechanism and facilitates the decay of pre-let-7. In the case of the mammalian miR-122, which is adenylated by cytoplasmic poly (A) polymerase GLD-2 (or also TUTase2), 3′-end adenylation is also implicated in its stabilization (134). Deep sequencing of the AGO-associated small RNAs has shown that adenylated miRNAs are relatively depleted in the AGO2 and AGO3 complexes, thereby suggesting that adenylation may interfere with AGO loading.

Single-nucleotide polymorphisms

Genetic variations range from large chromosomal anomalies to single-nucleotide changes. SNPs are the most frequently identified variants of DNA sequences. SNPs affecting miRNAs could potentially affect the maturation process of miRNAs, the silencing machinery, the structure or the expression level of mature miRNA, and the base pairing to target sites. Polymorphisms at a level of single nucleotides may also have functional roles in relation to miRNA-mediated gene regulation (135, 136). Screening by numerous bioinformatics analyses has so far demonstrated only a very low density of SNPs in miRNA profiles (103, 137). Polymorphisms in pre-miRNA may have an effect on miRNA maturation and thereby modulate miRNA expression. Several groups have tried to identify SNPs within or flanking pre-miRNA sequences using experimental or bioinformatics approaches. In one study, 173 human pre-miRNAs pertaining to 96 Japanese individuals were sequenced, identifying 10 SNPs in 10 pre-miRNA hairpins (138), yet another study identified 12 SNPs located within 227 human pre-miRNA sequences (139). Borel et al. (140) detected 65 SNPs in 49 pre-miRNAs but only in the case of three pre-miRNAs (hsa-miR-125a, hsa-miR-627 and hsa-miR-662) were the SNPs located within the seed region (140), thus demonstrating that SNPs within miRNA seed regions are very rare (~6%). Furthermore, a G-to-U polymorphism, located at the eighth nucleotide within the mature sequence of miR-125a, has been functionally characterized to block the processing of pri-miRNA into pre-miRNA, altering the translation suppression of the mRNA target, Lin28 (139). All of the above are good examples of the importance of the miRNA-related SNP.

Recently, the role of SNPs has been analyzed with reference to miRNA processing of cancer cells. For example, the hsa-miR-146a SNP (rs2910164) within the pre-miR146a sequence consists of one of the most thoroughly studied cases (135). This SNP reduces both the amount of pre-miR146a and mature hsa-miR-146a, ultimately affecting the DROSHA/DGCR8 cropping step, with consequent multiple associations to papillary thyroid carcinoma, familial/sporadic breast cancer, ovarian cancer, prostate cancer, and hepatocellular carcinoma (141–146). In addition, SNPs of mRNA located in the 3′ UTR region of the specific binding site of miRNAs induce regulation pattern changes of the corresponding transcript. An SNP located in the KRAS 3′ UTR induces the overexpression of KRAS, which has been correlated to an increased risk to acquire non-small-cell lung cancer due to the lack of miRNA let-7 binding (147). All of these studies have further contributed to the knowledge on miRNA binding site SNPs and cancer susceptibility; nonetheless, the need remains to carry out systematic studies to understand the role that SNPs play in connection to biological processes.

Expert opinion

The continuous progress in the quest to understand gene expression regulation mediated by small noncoding RNA, including miRNAs, is deeply revolutionizing our concepts in relation to the dynamics of functional genomics. The ubiquitous presence of these actors in the panorama of most biological processes, including pathologies, is offering new visions, new experimental approaches, and new perspectives with regard to the study of cellular and developmental biology. The multiple variants of the ‘miRNome’ are enhancing the world of fine regulation, the diversity, and the response to environmental changes experienced by biological systems. However, both the biogenesis and the real functionality of some of the described and annotated miRNAs deposited in the miRBase will need a further redefinition as has been recently proposed (148). The comprehension of the functional roles and possibilities of gene regulation by miRNAs has only just started.

Corresponding author: Jesús del Mazo, Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CIB), Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu, 9, E-28040 Madrid, Spain

About the authors

Jesús García-López

Jesus García-López holds a PhD from Complutense University of Madrid. At present he is doing postdoctoral research at the Laboratory of Molecular Biology of Gametogenesis CIB-CSIC, Madrid, Spain. He has previously worked on the RNA interference pathways and he is involved in the study of this small RNAs as biomarkers for embryo viability.

Miguel A. Brieño-Enríquez

Miguel A. Brieño-Enriquez, received his medical degree from Autonomous University of San Luis Potosi, Mexico, and his PhD from Autonomous University of Barcelona, Spain. His research includes the effects of endocrine disrupting chemicals on human fetal oocytes. At present, he is doing his postdoctoral research working on small RNAs and gonadal development at the Laboratory of Molecular Biology of Gametogenesis CIB-CSIC, Madrid, Spain.

Jesús del Mazo

Jesús del Mazo, PhD, is the Scientific Research and Group Leader of the ‘Molecular Biology of Gametogenesis’ Laboratory at Centre for Biological Research, CSIC, Madrid, Spain. From 1987 to 1989 he was an Associate Researcher at the California Institute of Technology, Pasadena, USA, and in 2006 he was an Honory Professor at Universidad de Valparaíso, Chile. He is the author of more than 60 articles in the field of Molecular Biology and Genetics of germ cells in mammals.

We thank R.M. Fratini for the English revision of the manuscript. Research on microRNAs carried out in del Mazo’s laboratory was supported by the following grants: CEFIC-LRi, MEDDTL (11-MRES-PNRPE-9-CVS-072), France, and CSIC (PIE 201020E016), Spain.

References

1. Axtell MJ, Westholm JO, Lai EC. Vive la difference: biogenesis and evolution of microRNAs in plants and animals. Genome Biol 2011; 12: 221.10.1186/gb-2011-12-4-221Search in Google Scholar

2. Griffiths-Jones S. The microRNA registry. Nucleic Acids Res 2004; 32: D109–11.10.1093/nar/gkh023Search in Google Scholar

3. Kozomara A, Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 2011; 39: D152–7.10.1093/nar/gkq1027Search in Google Scholar

4. Zhang R, Su B. Small but influential: the role of microRNAs on gene regulatory network and 3′ UTR evolution. J Genet Genomics 2009; 36: 1–6.10.1016/S1673-8527(09)60001-1Search in Google Scholar

5. Garcia-Lopez J, del Mazo J. Expression dynamics of microRNA biogenesis during preimplantation mouse development. Biochim Biophys Acta 2012; 1819: 847–54.10.1016/j.bbagrm.2012.03.007Search in Google Scholar PubMed

6. Hansen TB, Jensen TI, Clausen BH, Bramsen JB, Finsen B, Damgaard CK, Kjems J. Natural RNA circles function as efficient microRNA sponges. Nature 2013; 495: 384–8.10.1038/nature11993Search in Google Scholar PubMed

7. Ledford H. Circular RNAs throw genetics for a loop. Nature 2013; 494: 415.10.1038/494415aSearch in Google Scholar PubMed

8. Memczak S, Jens M, Elefsinioti A, Torti F, Krueger J, Rybak A, Maier L, Mackowiak SD, Gregersen LH, Munschauer M, Loewer A, Ziebold U, Landthaler M, Kocks C, le Noble F, Rajewsky N. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 2013; 495: 333–8.10.1038/nature11928Search in Google Scholar PubMed

9. Baccarini A, Chauhan H, Gardner TJ, Jayaprakash AD, Sachidanandam R, Brown BD. Kinetic analysis reveals the fate of a microrna following target regulation in mammalian cells. Curr Biol 2011; 21: 369–76.10.1016/j.cub.2011.01.067Search in Google Scholar PubMed PubMed Central

10. Kosik KS. Molecular biology: circles reshape the RNA world. Nature 2013; 495: 322–4.10.1038/nature11956Search in Google Scholar PubMed

11. Loinger A, Shemla Y, Simon I, Margalit H, Biham O. Competition between small RNAs: a quantitative view. Biophys J 2012; 102: 1712–21.10.1016/j.bpj.2012.01.058Search in Google Scholar

12. Chua JH, Armugam A, Jeyaseelan K. MicroRNAs: biogenesis, function and applications. Curr Opin Mol Ther 2009; 11: 189–99.Search in Google Scholar

13. Faller M, Guo F. MicroRNA biogenesis: there’s more than one way to skin a cat. Biochim Biophys Acta 2008; 1779: 663–7.10.1016/j.bbagrm.2008.08.005Search in Google Scholar

14. Cai Y, Yu X, Hu S, Yu J. A brief review on the mechanisms of miRNA regulation. Genom Proteom Bioinformat 2009; 7: 147–54.10.1016/S1672-0229(08)60044-3Search in Google Scholar

15. Chu CY, Rana TM. Small RNAs: regulators and guardians of the genome. J Cell Physiol 2007; 213: 412–9.10.1002/jcp.21230Search in Google Scholar PubMed

16. Davis BN, Hata A. Mechanisms of control of microRNA biogenesis. J Biochem 2010; 148: 381–92.Search in Google Scholar

17. Denli AM, Tops BB, Plasterk RH, Ketting RF, Hannon GJ. Processing of primary microRNAs by the Microprocessor complex. Nature 2004; 432: 231–5.10.1038/nature03049Search in Google Scholar PubMed

18. Gregory RI, Chendrimada TP, Shiekhattar R. MicroRNA biogenesis: isolation and characterization of the microprocessor complex. Methods Mol Biol 2006; 342: 33–47.10.1385/1-59745-123-1:33Search in Google Scholar

19. Bohnsack MT, Czaplinski K, Gorlich D. Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs. RNA 2004; 10: 185–91.10.1261/rna.5167604Search in Google Scholar PubMed PubMed Central

20. Lund E, Dahlberg JE. Substrate selectivity of exportin 5 and Dicer in the biogenesis of microRNAs. Cold Spring Harb Symp Quant Biol 2006; 71: 59–66.10.1101/sqb.2006.71.050Search in Google Scholar PubMed

21. Ohrt T, Merkle D, Birkenfeld K, Echeverri CJ, Schwille P. In situ fluorescence analysis demonstrates active siRNA exclusion from the nucleus by Exportin 5. Nucleic Acids Res 2006; 34: 1369–80.10.1093/nar/gkl001Search in Google Scholar PubMed PubMed Central

22. Chendrimada TP, Gregory RI, Kumaraswamy E, Norman J, Cooch N, Nishikura K, Shiekhattar R. TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature 2005; 436: 740–4.10.1038/nature03868Search in Google Scholar PubMed PubMed Central

23. Daniels SM, Melendez-Pena CE, Scarborough RJ, Daher A, Christensen HS, El Far M, Purcell DF, Laine S, Gatignol A. Characterization of the TRBP domain required for dicer interaction and function in RNA interference. BMC Mol Biol 2009; 10: 38.10.1186/1471-2199-10-38Search in Google Scholar PubMed PubMed Central

24. Okamura K, Liu N, Lai EC. Distinct mechanisms for microRNA strand selection by Drosophila Argonautes. Mol Cell 2009; 36: 431–44.10.1016/j.molcel.2009.09.027Search in Google Scholar PubMed PubMed Central

25. Shin C. Cleavage of the star strand facilitates assembly of some microRNAs into Ago2-containing silencing complexes in mammals. Mol Cell 2008; 26: 308–13.Search in Google Scholar

26. Chatterjee S, Grosshans H. Active turnover modulates mature microRNA activity in Caenorhabditis elegans. Nature 2009; 461: 546–9.10.1038/nature08349Search in Google Scholar PubMed

27. Eamens AL, Smith NA, Curtin SJ, Wang MB, Waterhouse PM. The Arabidopsis thaliana double-stranded RNA binding protein DRB1 directs guide strand selection from microRNA duplexes. RNA 2009; 15: 2219–35.10.1261/rna.1646909Search in Google Scholar PubMed PubMed Central

28. Miller S, Jones LE, Giovannitti K, Piper D, Serra MJ. Thermodynamic analysis of 5′ and 3′ single- and 3′ double-nucleotide overhangs neighboring wobble terminal base pairs. Nucleic Acids Res 2008; 36: 5652–9.10.1093/nar/gkn525Search in Google Scholar PubMed PubMed Central

29. O’Toole AS, Miller S, Haines N, Zink MC, Serra MJ. Comprehensive thermodynamic analysis of 3′ double-nucleotide overhangs neighboring Watson-Crick terminal base pairs. Nucleic Acids Res 2006; 34: 3338–44.10.1093/nar/gkl428Search in Google Scholar PubMed PubMed Central

30. Biasiolo M, Sales G, Lionetti M, Agnelli L, Todoerti K, Bisognin A, Coppe A, Romualdi C, Neri A, Bortoluzzi S. Impact of host genes and strand selection on miRNA and miRNA* expression. PLoS One 2011; 6: e23854.10.1371/journal.pone.0023854Search in Google Scholar PubMed PubMed Central

31. Joshua-Tor L. The Argonautes. Cold Spring Harb Symp Quant Biol 2006; 71: 67–72.10.1101/sqb.2006.71.048Search in Google Scholar PubMed

32. Mallory AC, Elmayan T, Vaucheret H. MicroRNA maturation and action – the expanding roles of ARGONAUTEs. Curr Opin Plant Biol 2008; 11: 560–6.10.1016/j.pbi.2008.06.008Search in Google Scholar PubMed

33. Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B, Abel L, Rappsilber J, Mann M, Dreyfuss G. miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev 2002; 16: 720–8.10.1101/gad.974702Search in Google Scholar PubMed PubMed Central

34. Peters L, Meister G. Argonaute proteins: mediators of RNA silencing. Mol Cell 2007; 26: 611–23.10.1016/j.molcel.2007.05.001Search in Google Scholar PubMed

35. Choe J, Cho H, Lee HC, Kim YK. microRNA/Argonaute 2 regulates nonsense-mediated messenger RNA decay. EMBO Rep 2010; 11: 380–6.10.1038/embor.2010.44Search in Google Scholar PubMed PubMed Central

36. Cifuentes D, Xue H, Taylor DW, Patnode H, Mishima Y, Cheloufi S, Ma E, Mane S, Hannon GJ, Lawson ND, Wolfe SA, Giraldez AJ. A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity. Science 2010; 328: 1694–8.10.1126/science.1190809Search in Google Scholar PubMed PubMed Central

37. Meister G, Landthaler M, Patkaniowska A, Dorsett Y, Teng G, Tuschl T. Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol Cell 2004; 15: 185–97.10.1016/j.molcel.2004.07.007Search in Google Scholar PubMed

38. Martin R, Smibert P, Yalcin A, Tyler DM, Schafer U, Tuschl T, Lai EC. A Drosophila pasha mutant distinguishes the canonical microRNA and mirtron pathways. Mol Cell Biol 2009; 29: 861–70.10.1128/MCB.01524-08Search in Google Scholar PubMed PubMed Central

39. Babiarz JE, Ruby JG, Wang Y, Bartel DP, Blelloch R. Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs. Genes Dev 2008; 22: 2773–85.10.1101/gad.1705308Search in Google Scholar PubMed PubMed Central

40. Chong MM, Zhang G, Cheloufi S, Neubert TA, Hannon GJ, Littman DR. Canonical and alternate functions of the microRNA biogenesis machinery. Genes Dev 2010; 24: 1951–60.10.1101/gad.1953310Search in Google Scholar PubMed PubMed Central

41. Ruby JG, Jan CH, Bartel DP. Intronic microRNA precursors that bypass Drosha processing. Nature 2007; 448: 83–6.10.1038/nature05983Search in Google Scholar PubMed PubMed Central

42. Okamura K, Hagen JW, Duan H, Tyler DM, Lai EC. The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila. Cell 2007; 130: 89–100.10.1016/j.cell.2007.06.028Search in Google Scholar PubMed PubMed Central

43. Curtis HJ, Sibley CR, Wood MJ. Mirtrons, an emerging class of atypical miRNA. Wiley Interdiscip Rev RNA 2012; 3: 617–32.10.1002/wrna.1122Search in Google Scholar PubMed

44. Berezikov E, Chung WJ, Willis J, Cuppen E, Lai EC. Mammalian mirtron genes. Mol Cell 2007; 28: 328–36.10.1016/j.molcel.2007.09.028Search in Google Scholar PubMed PubMed Central

45. Sibley CR, Seow Y, Saayman S, Dijkstra KK, El Andaloussi S, Weinberg MS, Wood MJ. The biogenesis and characterization of mammalian microRNAs of mirtron origin. Nucleic Acids Res 2012; 40: 438–48.10.1093/nar/gkr722Search in Google Scholar PubMed PubMed Central

46. Flynt AS, Greimann JC, Chung WJ, Lima CD, Lai EC. MicroRNA biogenesis via splicing and exosome-mediated trimming in Drosophila. Mol Cell 2010; 38: 900–7.10.1016/j.molcel.2010.06.014Search in Google Scholar PubMed PubMed Central

47. Glazov EA, Kongsuwan K, Assavalapsakul W, Horwood PF, Mitter N, Mahony TJ. Repertoire of bovine miRNA and miRNA-like small regulatory RNAs expressed upon viral infection. PLoS One 2009; 4: e6349.10.1371/journal.pone.0006349Search in Google Scholar PubMed PubMed Central

48. Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel DP. Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. Genes Dev 2010; 24: 992–1009.10.1101/gad.1884710Search in Google Scholar PubMed PubMed Central

49. Havens MA, Reich AA, Duelli DM, Hastings ML. Biogenesis of mammalian microRNAs by a non-canonical processing pathway. Nucleic Acids Res 2012; 40: 4626–40.10.1093/nar/gks026Search in Google Scholar PubMed PubMed Central

50. Cheloufi S, Dos Santos CO, Chong MM, Hannon GJ. A dicer-independent miRNA biogenesis pathway that requires Ago catalysis. Nature 2010; 465: 584–9.10.1038/nature09092Search in Google Scholar PubMed PubMed Central

51. Yang JS, Lai EC. Dicer-independent, Ago2-mediated microRNA biogenesis in vertebrates. Cell Cycle 2010; 9: 4455–60.10.4161/cc.9.22.13958Search in Google Scholar PubMed PubMed Central

52. Yang JS, Maurin T, Robine N, Rasmussen KD, Jeffrey KL, Chandwani R, Papapetrou EP, Sadelain M, O’Carroll D, Lai EC. Conserved vertebrate mir-451 provides a platform for Dicer-independent, Ago2-mediated microRNA biogenesis. Proc Natl Acad Sci USA 2010; 107: 15163–8.10.1073/pnas.1006432107Search in Google Scholar PubMed PubMed Central

53. Brameier M, Herwig A, Reinhardt R, Walter L, Gruber J. Human box C/D snoRNAs with miRNA like functions: expanding the range of regulatory RNAs. Nucleic Acids Res 2011; 39: 675–86.10.1093/nar/gkq776Search in Google Scholar PubMed PubMed Central

54. Ono M, Scott MS, Yamada K, Avolio F, Barton GJ, Lamond AI. Identification of human miRNA precursors that resemble box C/D snoRNAs. Nucleic Acids Res 2011; 39: 3879–91.10.1093/nar/gkq1355Search in Google Scholar PubMed PubMed Central

55. Ender C, Krek A, Friedlander MR, Beitzinger M, Weinmann L, Chen W, Pfeffer S, Rajewsky N, Meister G. A human snoRNA with microRNA-like functions. Mol Cell 2008; 32: 519–28.10.1016/j.molcel.2008.10.017Search in Google Scholar PubMed

56. Cole C, Sobala A, Lu C, Thatcher SR, Bowman A, Brown JW, Green PJ, Barton GJ, Hutvagner G. Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. RNA 2009; 15: 2147–60.10.1261/rna.1738409Search in Google Scholar PubMed PubMed Central

57. Gunaratne PH. Embryonic stem cell microRNAs: defining factors in induced pluripotent (iPS) and cancer (CSC) stem cells? Curr Stem Cell Res Ther 2009; 4: 168–77.10.2174/157488809789057400Search in Google Scholar PubMed

58. Keramari M, Razavi J, Ingman KA, Patsch C, Edenhofer F, Ward CM, Kimber SJ. Sox2 is essential for formation of trophectoderm in the preimplantation embryo. PLoS One 2010; 5: e13952.10.1371/journal.pone.0013952Search in Google Scholar PubMed PubMed Central

59. Rosa A, Brivanlou AH. A regulatory circuitry comprised of miR-302 and the transcription factors OCT4 and NR2F2 regulates human embryonic stem cell differentiation. EMBO J 2011; 30: 237–48.10.1038/emboj.2010.319Search in Google Scholar PubMed PubMed Central

60. Liu H, Deng S, Zhao Z, Zhang H, Xiao J, Song W, Gao F, Guan Y. Oct4 regulates the miR-302 cluster in P19 mouse embryonic carcinoma cells. Mol Biol Rep 2011; 38: 2155–60.10.1007/s11033-010-0343-4Search in Google Scholar PubMed

61. Card DA, Hebbar PB, Li L, Trotter KW, Komatsu Y, Mishina Y, Archer TK. Oct4/Sox2-regulated miR-302 targets cyclin D1 in human embryonic stem cells. Mol Cell Biol 2008; 28: 6426–38.10.1128/MCB.00359-08Search in Google Scholar PubMed PubMed Central

62. Lin SL, Chang DC, Lin CH, Ying SY, Leu D, Wu DT. Regulation of somatic cell reprogramming through inducible mir-302 expression. Nucleic Acids Res 2011; 39: 1054–65.10.1093/nar/gkq850Search in Google Scholar PubMed PubMed Central

63. Hermeking H. p53 enters the microRNA world. Cancer Cell 2007; 12: 414–8.10.1016/j.ccr.2007.10.028Search in Google Scholar PubMed

64. Ji Q, Hao X, Meng Y, Zhang M, Desano J, Fan D, Xu L. Restoration of tumor suppressor miR-34 inhibits human p53-mutant gastric cancer tumorspheres. BMC Cancer 2008; 8: 266.10.1186/1471-2407-8-266Search in Google Scholar PubMed PubMed Central

65. Tsai KW, Hu LY, Wu CW, Li SC, Lai CH, Kao HW, Fang WL, Lin WC. Epigenetic regulation of miR-196b expression in gastric cancer. Genes Chromosomes Cancer 2010; 49: 969–80.10.1002/gcc.20804Search in Google Scholar PubMed

66. Lehmann U, Hasemeier B, Christgen M, Muller M, Romermann D, Langer F, Kreipe H. Epigenetic inactivation of microRNA gene hsa-mir-9-1 in human breast cancer. J Pathol 2008; 214: 17–24.10.1002/path.2251Search in Google Scholar PubMed

67. Wang Z, Chen Z, Gao Y, Li N, Li B, Tan F, Tan X, Lu N, Sun Y, Sun J, Sun N, He J. DNA hypermethylation of microRNA-34b/c has prognostic value for stage non-small cell lung cancer. Cancer Biol Ther 2011; 11: 490–6.10.4161/cbt.11.5.14550Search in Google Scholar PubMed

68. George CX, Gan Z, Liu Y, Samuel CE. Adenosine deaminases acting on RNA, RNA editing, and interferon action. J Interferon Cytokine Res 2011; 31: 99–117.10.1089/jir.2010.0097Search in Google Scholar PubMed PubMed Central

69. Heale BS, Keegan LP, O’Connell MA. ADARs have effects beyond RNA editing. Cell Cycle 2009; 8: 4011–12.10.4161/cc.8.24.10214Search in Google Scholar PubMed

70. Hogg M, Paro S, Keegan LP, O’Connell MA. RNA editing by mammalian ADARs. Adv Genet 2011; 73: 87–120.10.1016/B978-0-12-380860-8.00003-3Search in Google Scholar PubMed

71. Zinshteyn B, Nishikura K. Adenosine-to-inosine RNA editing. Wiley Interdiscip Rev Syst Biol Med 2009; 1: 202–9.10.1002/wsbm.10Search in Google Scholar PubMed PubMed Central

72. Kawahara Y, Zinshteyn B, Chendrimada TP, Shiekhattar R, Nishikura K. RNA editing of the microRNA-151 precursor blocks cleavage by the Dicer-TRBP complex. EMBO Rep 2007; 8: 763–9.10.1038/sj.embor.7401011Search in Google Scholar PubMed PubMed Central

73. Kawahara Y, Zinshteyn B, Sethupathy P, Iizasa H, Hatzigeorgiou AG, Nishikura K. Redirection of Silencing Targets by Adenosine-to-Inosine Editing of miRNAs. Science 2007; 315: 1137–40.10.1126/science.1138050Search in Google Scholar PubMed PubMed Central

74. Garcia-Lopez J, Hourcade JD, del Mazo J. Reprogramming of microRNAs by adenosine-to-inosine editing and the selective elimination of edited microRNA precursors in mouse oocytes and preimplantation embryos. Nucleic Acids Res 2013; 41: 5483–93.10.1093/nar/gkt247Search in Google Scholar PubMed PubMed Central

75. Vesely C, Tauber S, Sedlazeck FJ, von Haeseler A, Jantsch MF. Adenosine deaminases that act on RNA induce reproducible changes in abundance and sequence of embryonic miRNAs. Genome Res 2012; 22: 1468–76.10.1101/gr.133025.111Search in Google Scholar PubMed PubMed Central

76. Guil S, Caceres JF. The multifunctional RNA-binding protein hnRNP A1 is required for processing of miR-18a. Nat Struct Mol Biol 2007; 14: 591–6.10.1038/nsmb1250Search in Google Scholar PubMed

77. Michlewski G, Guil S, Caceres JF. Stimulation of pri-miR-18a processing by hnRNP A1. Adv Exp Med Biol 2010; 700: 28–35.10.1007/978-1-4419-7823-3_3Search in Google Scholar PubMed

78. Paroo Z, Ye X, Chen S, Liu Q. Phosphorylation of the human microRNA-generating complex mediates MAPK/Erk signaling. Cell 2009; 139: 112–22.10.1016/j.cell.2009.06.044Search in Google Scholar PubMed PubMed Central

79. Chang TC, Zeitels LR, Hwang HW, Chivukula RR, Wentzel EA, Dews M, Jung J, Gao P, Dang CV, Beer MA, Thomas-Tikhonenko A, Mendell JT. Lin-28B transactivation is necessary for Myc-mediated let-7 repression and proliferation. Proc Natl Acad Sci USA 2009; 106: 3384–9.10.1073/pnas.0808300106Search in Google Scholar PubMed PubMed Central

80. Sempere LF, Freemantle S, Pitha-Rowe I, Moss E, Dmitrovsky E, Ambros V. Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation. Genome Biol 2004; 5: R13.10.1186/gb-2004-5-3-r13Search in Google Scholar PubMed PubMed Central

81. Wang YC, Chen YL, Yuan RH, Pan HW, Yang WC, Hsu HC, Jeng YM. Lin-28B expression promotes transformation and invasion in human hepatocellular carcinoma. Carcinogenesis 2010; 31: 1516–22.10.1093/carcin/bgq107Search in Google Scholar PubMed

82. Shyh-Chang N, Daley GQ. Lin28: primal regulator of growth and metabolism in stem cells. Cell Stem Cell 2013; 12: 395–406.10.1016/j.stem.2013.03.005Search in Google Scholar PubMed PubMed Central

83. Gonzalez-Gonzalez E, Lopez-Casas PP, del Mazo J. The expression patterns of genes involved in the RNAi pathways are tissue-dependent and differ in the germ and somatic cells of mouse testis. Biochim Biophys Acta 2008; 1779: 306–11.10.1016/j.bbagrm.2008.01.007Search in Google Scholar PubMed

84. Chatterjee S, Fasler M, Bussing I, Grosshans H. Target-mediated protection of endogenous micrornas in C. elegans. Dev Cell 2011; 20: 388–96.10.1016/j.devcel.2011.02.008Search in Google Scholar PubMed

85. Gu SG, Pak J, Barberan-Soler S, Ali M, Fire A, Zahler AM. Distinct ribonucleoprotein reservoirs for microRNA and siRNA populations in C. elegans. RNA 2007; 13: 1492–504.Search in Google Scholar

86. Poliseno L, Salmena L, Zhang J, Carver B, Haveman WJ, Pandolfi PP. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 2010; 465: 1033–8.10.1038/nature09144Search in Google Scholar PubMed PubMed Central

87. Ma J, Flemr M, Stein P, Berninger P, Malik R, Zavolan M, Svoboda P, Schultz RM. MicroRNA activity is suppressed in mouse oocytes. Curr Biol 2010; 20: 265–70.10.1016/j.cub.2009.12.042Search in Google Scholar PubMed PubMed Central

88. Muers M. Small RNAs: recycling for silencing. Nat Rev Genet 2011; 12: 227.10.1038/nrg2977Search in Google Scholar PubMed

89. Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M, Rajewsky N. Combinatorial microRNA target predictions. Nat Genet 2005; 37: 495–500.10.1038/ng1536Search in Google Scholar PubMed

90. Brennecke J, Stark A, Russell RB, Cohen SM. Principles of microRNA-target recognition. PLoS Biol 2005; 3: e85.10.1371/journal.pbio.0030085Search in Google Scholar PubMed PubMed Central

91. Brodersen P, Voinnet O. Revisiting the principles of microRNA target recognition and mode of action. Nat Rev Mol Cell Biol 2009; 10: 141–8.10.1038/nrm2619Search in Google Scholar PubMed

92. Rigoutsos I. New tricks for animal microRNAS: targeting of amino acid coding regions at conserved and nonconserved sites. Cancer Res 2009; 69: 3245–8.10.1158/0008-5472.CAN-09-0352Search in Google Scholar PubMed

93. John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS. Human MicroRNA targets. PLoS Biol 2004; 2: e363.10.1371/journal.pbio.0020363Search in Google Scholar PubMed PubMed Central

94. Rajewsky N. microRNA target predictions in animals. Nat Genet 2006; 38: S8–13.10.1038/ng1798Search in Google Scholar PubMed

95. Friedman RC, Farh KK, Burge CB, Bartel DP. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 2009; 19: 92–105.10.1101/gr.082701.108Search in Google Scholar PubMed PubMed Central

96. Das AK, Carmichael GG. ADAR editing wobbles the microRNA world. ACS Chem Biol 2007; 2: 217–20.10.1021/cb700064hSearch in Google Scholar PubMed

97. O’Connell MA, Keegan LP. Drosha versus ADAR: wrangling over pri-miRNA. Nat Struct Mol Biol 2006; 13: 3–4.10.1038/nsmb0106-3Search in Google Scholar PubMed

98. Yang W, Chendrimada TP, Wang Q, Higuchi M, Seeburg PH, Shiekhattar R, Nishikura K. Modulation of microRNA processing and expression through RNA editing by ADAR deaminases. Nat Struct Mol Biol 2006; 13: 13–21.10.1038/nsmb1041Search in Google Scholar PubMed PubMed Central

99. Luciano DJ, Mirsky H, Vendetti NJ, Maas S. RNA editing of a miRNA precursor. RNA 2004; 10: 1174–7.10.1261/rna.7350304Search in Google Scholar PubMed PubMed Central

100. Kawahara Y, Megraw M, Kreider E, Iizasa H, Valente L, Hatzigeorgiou AG, Nishikura K. Frequency and fate of microRNA editing in human brain. Nucleic Acids Res 2008; 36: 5270–80.10.1093/nar/gkn479Search in Google Scholar PubMed PubMed Central

101. Scadden AD. The RISC subunit Tudor-SN binds to hyper-edited double-stranded RNA and promotes its cleavage. Nat Struct Mol Biol 2005; 12: 489–96.10.1038/nsmb936Search in Google Scholar PubMed

102. Weissbach R, Scadden AD. Tudor-SN and ADAR1 are components of cytoplasmic stress granules. RNA 2012; 18: 462–71.10.1261/rna.027656.111Search in Google Scholar PubMed PubMed Central

103. Saunders MA, Liang H, Li WH. Human polymorphism at microRNAs and microRNA target sites. Proc Natl Acad Sci USA 2007; 104: 3300–5.10.1073/pnas.0611347104Search in Google Scholar PubMed PubMed Central

104. Ohman M. A-to-I editing challenger or ally to the microRNA process. Biochimie 2007; 89: 1171–6.10.1016/j.biochi.2007.06.002Search in Google Scholar PubMed

105. Neilsen CT, Goodall GJ, Bracken CP. IsomiRs – the overlooked repertoire in the dynamic microRNAome. Trends Genet 2012; 28: 544–9.10.1016/j.tig.2012.07.005Search in Google Scholar PubMed

106. Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V, Chiaretti S, Foà R, Schliwka J, Fuchs U, Novosel A, Müller RU, Schermer B, Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G, Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN, Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo JJ, Sander C, Zavolan M, Tuschl T. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 2007; 129: 1401–14.10.1016/j.cell.2007.04.040Search in Google Scholar PubMed PubMed Central

107. Ebhardt HA, Tsang HH, Dai DC, Liu Y, Bostan B, Fahlman RP. Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications. Nucleic Acids Res 2009; 37: 2461–70.10.1093/nar/gkp093Search in Google Scholar PubMed PubMed Central

108. Cloonan N, Wani S, Xu Q, Gu J, Lea K, Heater S, Barbacioru C, Steptoe AL, Martin HC, Nourbakhsh E, Krishnan K, Gardiner B, Wang X, Nones K, Steen JA, Matigian NA, Wood DL, Kassahn KS, Waddell N, Shepherd J, Lee C, Ichikawa J, McKernan K, Bramlett K, Kuersten S, Grimmond SM. MicroRNAs and their isomiRs function cooperatively to target common biological pathways. Genome Biol 2011; 12: R126.10.1186/gb-2011-12-12-r126Search in Google Scholar PubMed PubMed Central

109. Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC. Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res 2007; 17: 1850–64.10.1101/gr.6597907Search in Google Scholar PubMed PubMed Central

110. Berezikov E, Robine N, Samsonova A, Westholm JO, Naqvi A, Hung JH, Okamura K, Dai Q, Bortolamiol-Becet D, Martin R, Zhao Y, Zamore PD, Hannon GJ, Marra MA, Weng Z, Perrimon N, Lai EC. Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. Genome Res 2011; 21: 203–15.10.1101/gr.116657.110Search in Google Scholar PubMed PubMed Central

111. Lee LW, Zhang S, Etheridge A, Ma L, Martin D, Galas D, Wang K. Complexity of the microRNA repertoire revealed by next-generation sequencing. RNA 2010; 16: 2170–80.10.1261/rna.2225110Search in Google Scholar PubMed PubMed Central

112. Wyman SK, Knouf EC, Parkin RK, Fritz BR, Lin DW, Dennis LM, Krouse MA, Webster PJ, Tewari M. Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity. Genome Res 2011; 21: 1450–61.10.1101/gr.118059.110Search in Google Scholar PubMed PubMed Central

113. Burroughs AM, Ando Y, de Hoon MJ, Tomaru Y, Nishibu T, Ukekawa R, Funakoshi T, Kurokawa T, Suzuki H, Hayashizaki Y, Daub CO. A comprehensive survey of 3′ animal miRNA modification events and a possible role for 3′ adenylation in modulating miRNA targeting effectiveness. Genome Res 2010; 20: 1398–410.10.1101/gr.106054.110Search in Google Scholar PubMed PubMed Central

114. Newman MA, Mani V, Hammond SM. Deep sequencing of microRNA precursors reveals extensive 3′ end modification. RNA 2011; 17: 1795–803.10.1261/rna.2713611Search in Google Scholar PubMed PubMed Central

115. Fernandez-Valverde SL, Taft RJ, Mattick JS. Dynamic isomiR regulation in Drosophila development. RNA 2010; 16: 1881–8.10.1261/rna.2379610Search in Google Scholar PubMed PubMed Central

116. Park JE, Heo I, Tian Y, Simanshu DK, Chang H, Jee D, Patel DJ, Kim VN. Dicer recognizes the 5′ end of RNA for efficient and accurate processing. Nature 2011; 475: 201–205.10.1038/nature10198Search in Google Scholar PubMed PubMed Central

117. Parker JS. The generation of small RNAs; who needs Dicer? J RNAi Gene Silencing 2007; 3: 215–6.Search in Google Scholar

118. Vermeulen A, Behlen L, Reynolds A, Wolfson A, Marshall WS, Karpilow J, Khvorova A. The contributions of dsRNA structure to Dicer specificity and efficiency. RNA 2005; 11: 674–82.10.1261/rna.7272305Search in Google Scholar PubMed PubMed Central

119. Wu H, Ye C, Ramirez D, Manjunath N. Alternative processing of primary microRNA transcripts by Drosha generates 5′ end variation of mature microRNA. PLoS One 2009; 4: e7566.10.1371/journal.pone.0007566Search in Google Scholar PubMed PubMed Central

120. Kuchenbauer F, Morin RD, Argiropoulos B, Petriv OI, Griffith M, Heuser M, Yung E, Piper J, Delaney A, Prabhu AL, Zhao Y, McDonald H, Zeng T, Hirst M, Hansen CL, Marra MA, Humphries RK. In-depth characterization of the microRNA transcriptome in a leukemia progression model. Genome Res 2008; 18: 1787–97.10.1101/gr.077578.108Search in Google Scholar PubMed PubMed Central

121. Zhou H, Arcila ML, Li Z, Lee EJ, Henzler C, Liu J, Rana TM, Kosik KS. Deep annotation of mouse iso-miR and iso-moR variation. Nucleic Acids Res 2012; 40: 5864–75.10.1093/nar/gks247Search in Google Scholar PubMed PubMed Central

122. Starega-Roslan J, Koscianska E, Kozlowski P, Krzyzosiak WJ. The role of the precursor structure in the biogenesis of microRNA. Cell Mol Life Sci 2011; 68: 2859–71.10.1007/s00018-011-0726-2Search in Google Scholar PubMed PubMed Central

123. Starega-Roslan J, Krzyzosiak WJ. Analysis of microRNA length variety generated by recombinant human Dicer. Methods Mol Biol 2013; 936: 21–34.10.1007/978-1-62703-083-0_2Search in Google Scholar PubMed

124. Liu N, Abe M, Sabin LR, Hendriks GJ, Naqvi AS, Yu Z, Cherry S, Bonini NM. The exoribonuclease Nibbler controls 3′ end processing of microRNAs in Drosophila. Curr Biol 2011; 21: 1888–93.10.1016/j.cub.2011.10.006Search in Google Scholar PubMed PubMed Central

125. Han BW, Hung JH, Weng Z, Zamore PD, Ameres SL. The 3′-to-5′ exoribonuclease Nibbler shapes the 3′ ends of microRNAs bound to Drosophila Argonaute1. Curr Biol 2011; 21: 1878–87.10.1016/j.cub.2011.09.034Search in Google Scholar PubMed PubMed Central

126. Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 2006; 127: 1193–207.10.1016/j.cell.2006.10.040Search in Google Scholar PubMed

127. Li J, Yang Z, Yu B, Liu J, Chen X. Methylation protects miRNAs and siRNAs from a 3′-end uridylation activity in Arabidopsis. Curr Biol 2005; 15: 1501–7.10.1016/j.cub.2005.07.029Search in Google Scholar PubMed PubMed Central

128. Yu B, Yang Z, Li J, Minakhina S, Yang M, Padgett RW, Steward R, Chen X. Methylation as a crucial step in plant microRNA biogenesis. Science 2005; 307: 932–5.10.1126/science.1107130Search in Google Scholar PubMed PubMed Central

129. Martin G, Keller W. RNA-specific ribonucleotidyl transferases. RNA 2007; 13: 1834–49.10.1261/rna.652807Search in Google Scholar PubMed PubMed Central

130. Westholm JO, Ladewig E, Okamura K, Robine N, Lai EC. Common and distinct patterns of terminal modifications to mirtrons and canonical microRNAs. RNA 2012; 18: 177–92.10.1261/rna.030627.111Search in Google Scholar PubMed PubMed Central

131. Heo I, Joo C, Cho J, Ha M, Han J, Kim VN. Lin28 mediates the terminal uridylation of let-7 precursor MicroRNA. Mol Cell 2008; 32: 276–84.10.1016/j.molcel.2008.09.014Search in Google Scholar PubMed

132. Chang HM, Triboulet R, Thornton JE, Gregory RI. A role for the Perlman syndrome exonuclease Dis3l2 in the Lin28-let-7 pathway. Nature 2013; 497:244–8.10.1038/nature12119Search in Google Scholar PubMed PubMed Central

133. Heo I, Joo C, Kim YK, Ha M, Yoon MJ, Cho J, Yeom KH, Han J, Kim VN. TUT4 in concert with Lin28 suppresses microRNA biogenesis through pre-microRNA uridylation. Cell 2009; 138: 696–708.10.1016/j.cell.2009.08.002Search in Google Scholar PubMed

134. Katoh T, Sakaguchi Y, Miyauchi K, Suzuki T, Kashiwabara S, Baba T. Selective stabilization of mammalian microRNAs by 3′ adenylation mediated by the cytoplasmic poly(A) polymerase GLD-2. Genes Dev 2009; 23: 433–8.10.1101/gad.1761509Search in Google Scholar PubMed PubMed Central

135. Jazdzewski K, de la Chapelle A. Genomic sequence matters: a SNP in microRNA-146a can turn anti-apoptotic. Cell Cycle 2009; 8: 1642–3.10.4161/cc.8.11.8621Search in Google Scholar

136. Mishra PJ, Banerjee D, Bertino JR. MiRSNPs or MiR-polymorphisms, new players in microRNA mediated regulation of the cell: introducing microRNA pharmacogenomics. Cell Cycle 2008; 7: 853–8.10.4161/cc.7.7.5666Search in Google Scholar PubMed

137. Chen K, Rajewsky N. Natural selection on human microRNA binding sites inferred from SNP data. Nat Genet 2006; 38: 1452–6.10.1038/ng1910Search in Google Scholar PubMed

138. Iwai N, Naraba H. Polymorphisms in human pre-miRNAs. Biochem Biophys Res Commun 2005; 331: 1439–44.10.1016/j.bbrc.2005.04.051Search in Google Scholar PubMed

139. Duan R, Pak C, Jin P. Single nucleotide polymorphism associated with mature miR-125a alters the processing of pri-miRNA. Hum Mol Genet 2007; 16: 1124–31.10.1093/hmg/ddm062Search in Google Scholar PubMed

140. Borel F, Konstantinova P, Jansen PL. Diagnostic and therapeutic potential of miRNA signatures in patients with hepatocellular carcinoma. J Hepatol 2012; 56: 1371–83.10.1016/j.jhep.2011.11.026Search in Google Scholar PubMed

141. Jazdzewski K, Murray EL, Franssila K, Jarzab B, Schoenberg DR, de la Chapelle A. Common SNP in pre-miR-146a decreases mature miR expression and predisposes to papillary thyroid carcinoma. Proc Natl Acad Sci USA 2008; 105: 7269–74.10.1073/pnas.0802682105Search in Google Scholar PubMed PubMed Central

142. Jazdzewski K, Liyanarachchi S, Swierniak M, Pachucki J, Ringel MD, Jarzab B, de la Chapelle A. Polymorphic mature microRNAs from passenger strand of pre-miR-146a contribute to thyroid cancer. Proc Natl Acad Sci USA 2009; 106: 1502–5.10.1073/pnas.0812591106Search in Google Scholar PubMed PubMed Central

143. Xu B, Feng NH, Li PC, Tao J, Wu D, Zhang ZD, Tong N, Wang JF, Song NH, Zhang W, Hua LX, Wu HF. A functional polymorphism in Pre-miR-146a gene is associated with prostate cancer risk and mature miR-146a expression in vivo. Prostate 2010; 70: 467–72.10.1002/pros.21080Search in Google Scholar PubMed

144. Amir S, Ma AH, Shi XB, Xue L, Kung HJ, Devere White RW. Oncomir miR-125b suppresses p14(ARF) to modulate p53-dependent and p53-independent apoptosis in prostate cancer. PLoS One 2013; 8: e61064.10.1371/journal.pone.0061064Search in Google Scholar PubMed PubMed Central

145. Shen J, Ambrosone CB, DiCioccio RA, Odunsi K, Lele SB, Zhao H. A functional polymorphism in the miR-146a gene and age of familial breast/ovarian cancer diagnosis. Carcinogenesis 2008; 29: 1963–6.10.1093/carcin/bgn172Search in Google Scholar PubMed

146. Hu Z, Liang J, Wang Z, Tian T, Zhou X, Chen J, Miao R, Wang Y, Wang X, Shen H. Common genetic variants in pre-microRNAs were associated with increased risk of breast cancer in Chinese women. Hum Mutat 2009; 30: 79–84.10.1002/humu.20837Search in Google Scholar PubMed

147. Chin LJ, Ratner E, Leng S, Zhai R, Nallur S, Babar I, Muller RU, Straka E, Su L, Burki EA, Crowell RE, Patel R, Kulkarni T, Homer R, Zelterman D, Kidd KK, Zhu Y, Christiani DC, Belinsky SA, Slack FJ, Weidhaas JB. A SNP in a let-7 microRNA complementary site in the KRAS 3′ untranslated region increases non-small cell lung cancer risk. Cancer Res 2008; 68: 8535–40.10.1158/0008-5472.CAN-08-2129Search in Google Scholar PubMed PubMed Central

148. Castellano L, Stebbing J. Deep sequencing of small RNAs identifies canonical and non-canonical miRNA and endogenous siRNAs in mammalian somatic tissues. Nucleic Acids Res 2013; 41: 3339–51.10.1093/nar/gks1474Search in Google Scholar PubMed PubMed Central

Received: 2013-5-27

Accepted: 2013-6-20

Published Online: 2013-08-02

Published in Print: 2013-08-01

This article is distributed under the terms of the Creative Commons Attribution Non-Commercial License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles in the same Issue

https://doi.org/10.1515/bmc-2013-0015

Keywords for this article

canonical biogenesis; editing; microRNAs; noncanonical biogenesis; isomiRs

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