2016 micro rna in control of gene expression an overview of nuclear functions

International Journal of
Molecular Sciences
Review
MicroRNA in Control of Gene Expression:
An Overview of Nuclear Functions
Caterina Catalanotto *,†, Carlo Cogoni *,† and Giuseppe Zardo *,†
Department of Cellular Biotechnologies and Hematology, University of Rome Sapienza, Rome 00179, Italy
* Correspondence: caterina.catalanotto@uniroma1.it (Ca.Ca.); carlo.cogoni@uniroma1.it (Ca.Co.);
giuseppe.zardo@uniroma1.it (G.Z.); Tel.: +39-064-991-8247 (G.Z.); Fax: +39-064-991-8251 (G.Z.)
† These authors contributed equally to this work.
Academic Editor: Y-h. Taguchi
Received: 26 August 2016; Accepted: 7 October 2016; Published: 13 October 2016
Abstract: The finding that small non-coding RNAs (ncRNAs) are able to control gene expression
in a sequence specific manner has had a massive impact on biology. Recent improvements in high
throughput sequencing and computational prediction methods have allowed the discovery and
classification of several types of ncRNAs. Based on their precursor structures, biogenesis pathways
and modes of action, ncRNAs are classified as small interfering RNAs (siRNAs), microRNAs
(miRNAs), PIWI-interacting RNAs (piRNAs), endogenous small interfering RNAs (endo-siRNAs or
esiRNAs), promoter associate RNAs (pRNAs), small nucleolar RNAs (snoRNAs) and sno-derived
RNAs. Among these, miRNAs appear as important cytoplasmic regulators of gene expression.
miRNAs act as post-transcriptional regulators of their messenger RNA (mRNA) targets via mRNA
degradation and/or translational repression. However, it is becoming evident that miRNAs also have
specific nuclear functions. Among these, the most studied and debated activity is the miRNA-guided
transcriptional control of gene expression. Although available data detail quite precisely the effectors
of this activity, the mechanisms by which miRNAs identify their gene targets to control transcription
are still a matter of debate. Here, we focus on nuclear functions of miRNAs and on alternative
mechanisms of target recognition, at the promoter lavel, by miRNAs in carrying out transcriptional
gene silencing.
Keywords: microRNA; miRNA inducing silencing complex (miRISC); transcriptional control;
epigenetics; nuclear function
1. Biogenesis of miRNAs
The most studied class of small non-coding RNAs (ncRNA) are the miRNAs. They are encoded
within the genomes of organisms ranging from plants to animals. It has been estimated that they are
able to modulate up to 60% of protein-coding genes in the human genome at the translational level [1].
Because of their ubiquitous role in gene regulation, they are involved in many physiological processes,
such as differentiation, proliferation, apoptosis and development, and their dysregulation has been
related to various pathological disorders, including muscular dystrophy [2], diabetes [3] and several
types of cancer [4].
Biogenesis of miRNAs occurs through a multi-step process requiring both a nuclear and
a cytoplasmic phase. They are transcribed typically by RNA polymerases II or III as long primary
miRNA (pri-miRNA) with a cap and a poly-A tail. pri-miRNAs contain a double-stranded stem of
about 30 base pairs, a terminal loop and two flanking unstructured single-stranded tails. pri-miRNAs
are processed into short 70-nt stem-loop structures known as precursor miRNAs (pre-miRNAs) by
a protein complex, the Microprocessor complex, which consists of the RNase III enzyme Drosha,
and a double stranded-RNA binding protein, Di George syndrome critical region 8 gene (DGCR8).
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Int. J. Mol. Sci. 2016, 17, 1712 2 of 17
Further processing of pre-miRNAs by the RNase III enzyme Dicer generates miRNA duplexes
(ds-miRNAs) [5,6] with a phosphate at the 5 end and a 2-nt overhang with a hydroxyl at the 3 end [7–9].
The miRNA duplex, is successively loaded onto Argonaute (AGO) itself by an RNA inducing silencing
complex (RISC) comprising Dicer, trans-activation response RNA-binding protein (TRBP) and AGO.
TRBP identifies the “guide” and the “passenger” strands in the ds-miRNA molecule. TRBP senses the
thermodynamic properties of the ds-miRNAs, and once it recognizes the strand with the less stable
5 end, the protein loads the ds-miRNA in the correct orientation onto AGO proteins. AGO unwinds
the duplex, and removes the passenger strand retaining the mature miRNA molecule [5,10]. A subclass
of miRNAs, called mirtrons, bypass the initial Drosha cleavage and instead depend on splicing and
debranching to produce the pre-miRNA molecules which are the substrates for Dicer mediated miRNA
maturation [11,12]. Another subset of miRNAs originating in short introns, agotrons, has been recently
characterized [13]. Mature agotrons are similar to pre-miRNAs (80–100 nt), and their biogenesis is
independent of both Drosha and Dicer although they are ultimately associated and stabilized by
Argonaute (AGO) proteins [14]. pre-miRNAs are translocated to the cytoplasm in a process mediated
by Exportin5 (XPO5), a member of the karyopherin β family, in a complex with Ran·GTPase [15].
2. Function of Cytoplasmic miRNAs
In plants, and rarely in mammals, perfect complementarity between miRNA and target mRNA
induces the cleavage and disruption of the latter [16]. In animals, seminal studies on miRNAs have
shown that only the seed region (sequence spanning from position 2 to 8 at the 5 end), is crucial for
target recognition. The seed sequence pairs fully to its responsive element mainly at the 3 untranslated
region (UTR) of the target mRNA [17]. However, miRNA responsive elements (MREs) are also
ubiquitously widespread in 5 UTR sequences as well as in coding regions of mRNAs [18–20]. Moreover,
recent advances in the transcriptome-wide method of mapping miRNA binding sites (AGO HITS-CLIP)
demonstrated that a number of miRNA-target interactions in vivo are mediated through non-canonical
seed pairing rules (~15%–80%) [21,22].
The cornerstone of the miRNA functioning is the formation of the RISC composing minimally
of an AGO protein and a miRNA molecule. The utility of this binary complex is highlighted by the
following factors: (i) miRNAs can specifically recognize their mRNA targets through Watson and Crick
base pairing, and at the same time, may easily detach and reattach to different targets, thus exerting
their control serially on a wide range of target molecules; (ii) the AGO proteins provide an extremely
efficient platform onto which modulating cofactors can bind their targets. Whereas miRNA is
responsible for recognizing the mRNA target to be modulated, the task of AGO proteins is to determine
the mode of action of the RISC-mediated gene regulation. Despite their high sequence similarity
and the fact that critical aminoacids are conserved also in other AGO proteins, only AGO2 possesses
endonuclease activity, if the miRNA-mRNA base pairing is perfect [23,24]. It is, therefore, still uncertain
what the exact functions of the different AGO proteins are.
The endonucleolytic ability to degrade cellular mRNAs is not frequently adopted by mammalian
RISCs. Most often, the minimal RISC (AGO2 and miRNA) acts as a platform to recruit proteins that
define the fate of the RISC’s target mRNAs [24–26]. These factors have been grouped according to
their biological functions as: proteins required for RISC assembly, proteins involved in translational
regulation, messenger RNA-binding proteins and proteins involved in RNA metabolism. Therefore,
in addition to those factors closely required to build a functional minimal RISC (i.e., Dicer, TRBP and
Hsp90 proteins, allowing incorporation of the miRNAs into the RISC) a large group of AGO interacting
proteins is necessary to explain the mechanism of RISC mediated gene regulation in animals.
3. miRNA-RISC: Cytoplasmic Activity
Since its discovery 20 years ago, the primary function of the miRNA-RISC (miRISC) appeared to be
post-transcriptional mRNA regulation in the cytoplasm. Several models have been proposed to explain
the mechanism used by the miRNA-RISC complex to control mRNA fate. In general, miRISCs either

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hinder translation or enhance mRNA degradation. For a long time, the predominant idea was that
variation in the composition of RISCs led to alternative mechanisms for post-transcriptional control.
More recently, the outlook has changed. The current model proposes that, in a sequential process,
the RISC switches off its targets by repressing mRNA translation at first and subsequently initiating
degradation [27]. However, it has been suggested that the sequential order of these two events reflects
kinetic differences between translational repression and mRNA decay rather than a cause-and-effect
relationship between them [27–29].
Ribosome-profiling experiments [30] and polysome profiling combined with high-throughput
sequencing methods ruled out that miRISC post-transcriptional control occurs through inhibition
of translation elongation, protein degradation or ribosome drop-off. In addition, Bazzini et al. [29]
found that miR-430 reduces the number of ribosomes on target mRNAs in wild type and Dicer
mutant zebrafish embryos indicating that miRNAs can regulate translation at an initiation step.
Removal of the poly(A) tail did not affect miRISC dependent translational repression suggesting
that miRISC induced deadenylation represents a level of miRNA mediated control independent
from translation. The opposite is also true; miRNA guided translational repression is not required
for miRNA dependent deadenylation [31]. Béthune et al. [32] provided further support for these
observations, showing that translational repression is the dominant effect on newly synthesized
targets, whereas mRNA deadenylation and decay are prevalent at steady state.
However, in quantitative terms, destabilization of target mRNAs is the main cause for reduced
protein output. In fact, translational repression provides roughly 6%–25% of the global repression in
protein expression [33,34]. In recent years, the CCR4-NOT complex has been identified as the main
effector downstream of the RISC complex. The CCR4–NOT complex coordinates mRNA deadenylation
directly and indirectly, by recruiting PABP proteins or DEAD box helicases, such as eIF1A and
DDX6, mRNA decapping and translational repression. Thus, several authors have explored the
details of the mechanistic events and protein effectors regulating miRNA mediated target decay and
translational repression shedding light on miRISC activity in the cytoplasm (for a review see Jonas and
Izaurralde [35]).
4. miRISC and miRNAs: Cytoplasmic/Nuclear Shuttling
Within the last few years, there have been several reports indicating that miRISC complexes
are also present in mammalian cell nuclei. Western blots of nuclear fractions, cell fractionation and
immunofluorescence have revealed the presence of AGO proteins, Dicer, TRBP, and Gw182/TNRC6 in
cell nuclei [36–39], where they combine to form multi-proteins complexes [40]. By performing protein
fractionation and ammonium sulphate precipitation assays on HeLa nuclear and cytoplasmic extracts,
Gagnon and co-workers [40] suggested that the composition of miRISC complexes and binding stability
of their components differ in the nucleus relative to the cytoplasm. At the same time, they found that
the nuclear Dicer programmed with exogenous 21-nt siRNAs retains its catalytic activity as well as
AGO2, and is able to target nuclear RNAs, such as 7SK small nucleolar RNAs (snoRNA), inducing its
degradation [40]. However, the loading process appeared to occur in the cytoplasm, despite the
simultaneous presence of Dicer and TRBP within the nucleus. The current hypothesis is that the
miRNA-AGO2 assembly occurs outside the nucleus, where some critical loading factors are present.
Once established, the minimal RISC may subsequently be imported into the nucleus. This assumption
is in accordance with previous analysis suggesting that the nuclear RISC seems to be smaller than its
cytoplasmic counterpart [37]. More recently, using a semi quantitative mass spectrometry approach,
Kalantari et al. [41] have confirmed the small size of the nuclear RISC, showing that the association of
AGO2 with Gw182/TNRC6 (-A, -B, -C) and AGO3 is best preserved and more stable in both nuclei and
cytoplasm whereas the AGO2 interaction with Dicer and TRBP is confined to the cytoplasm. Obviously,
different conditions for biochemical purification may yield diverse compositions of the RISC.
These observations overall suggest that the minimal RISC might constitute the core component of
a larger machinery designed to modulate gene expression also in the nucleus. However, the mechanism

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guiding the cytoplasmic-nuclear shuttling of miRISC remains an open question. A family of
proteins, called karyopherins, mediates the translocation of the RISC into the nucleus. These proteins
recognize nuclear localization sequences in the protein cargoes and then assist their active transport
through the nuclear pore complex. In detail, the AGO-miRNA complex is imported into the
nucleus by binding to importin 8 (IPO8) [38,42]. In fact, silencing of IPO8 reduces the pool of
nuclear AGO2 [38]. AGO2 is lacking a nuclear localization signal unlike many components of the
cytoplasmic RISC, including TNRC6 paralogs and Dicer [39–43], although a recent paper questions
Dicer nuclear compartmentalization [44]. However, AGO2 overcomes this deficiency by combining
with TNRC6A which possesses a nuclear localization signal (NLS) rather than a nuclear export signal
(NES), and works as a nuclear–cytoplasmic shuttling protein to re-localize minimal miRISC to the
nucleus [39,45]. It is possible that IPO8, TNRC6A and AGO2 localize together in cytoplasmic P-bodies
where they form a final complex capable of binding to nuclear pore complex (NPC) entering the
nucleus. On the other hand, the NES element of TNRC6A affects AGO2 nuclear export. Indeed,
inhibition of exportin1 (XPO1) results in nuclear accumulation of both of these proteins [39,46].
The basic idea is that the RISC can undertake more than one route to reach the nuclear
compartment. In parallel with the identification of nuclear RISCs, miRNAs have been detected
in the nuclear compartment through microarray analysis and small RNA deep sequencing of nuclear
extracts [47–50]. Gagnon and co-workers [40] have found that about 75% of whole cell miRNAs are
present in both the nucleus and the cytoplasm. They also demonstrated that the relative abundance of
miRNAs in the cytoplasm reflects their relative proportion in the nucleus also, suggesting an inability of
the miRNA cytoplasmic-nuclear shuttling mechanisms to internalize specific miRNAs. Several studies
have shown that nuclear miRNAs co-localize with TNRC6A [39], which is a main component of
cytoplasmic miRISC. This finding has given rise to the idea that miRNAs can be relocated to the
nucleus through miRISC shuttling.
In contrast to the hypothesis of an unselective distribution of miRNAs, several studies have
suggested the existence of a motif-dependent mechanism that selectively translocates miRNAs into the
nucleus. For instance, a seminal study reported that a hexanucleotide element (AGUGUU) at the 3 end
of miR-29b is responsible for its selective nuclear localization in HeLa cells. Indeed, translocation of
this 6-nt motif to other small RNAs is able to induce their nuclear accumulation [51]. Subsequent work
has partially confirmed the importance of the 3 -terminal sequences in defining cellular localization of
mature miRNAs. In addition, it has been suggested that the miRNAs containing a 3 ASUS element
(where S may be a cytosine or guanosine) or a 3 -terminal guanine nucleotide, which can be added in
a non-template manner, are preferentially localized within the nucleus [49,50]. Therefore, it is possible
that machinery involved in a motif-dependent miRNA nuclear translocation, able to grant nuclear
access of specific miRNAs, exists. However, data from different laboratories suggest that whatever
the selective system of miRNA nuclear translocation is, it may be differentially expressed in various
cell types. Indeed, the pool of miRNAs enriched in the nuclei appears to be cell line specific. It is
also useful to consider some data demonstrating that exogenous siRNAs are preferentially able to
localize to the cytoplasm or to the nucleus in a manner dependent on the trapping activity of their
targets [52,53]. They move back and forth between nucleus and cytoplasm, and they are retained in
the cellular compartment where they identify their target molecules.
5. miRNAs: Nuclear Functions
Some results demonstrate that miRNA may have different nuclear functions, in some cases,
independent of RISC activity. Actually, only a limited number of miRNAs are representative of these
non-canonical roles, and little is known about their mode of action.
5.1. Regulation of RNA Transcriptome
miRISCs were found to induce post-transcriptional degradation of small RNA molecules, such as
long non-coding RNAs confined to the nucleus. For example, the nuclear miR-709 seems to inhibit

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miRNA15a/16-1 maturation by binding to a 19-nt recognition element on pri-miR-15a/16-1 and thus
blocking its processing into pre-miR-15a/16-1 in mouse cells [54]. In a similar manner, the mature
let-7 miRNA in Caenorhabditis elegans physically associates with its own pri-miRNA within the nucleus
promoting the processing of the pri-miRNA transcript, and thus providing a positive feedback
loop [55].
An unbiased analysis of miRNA-mRNA-Argonaute interactions in mouse brain using
high-throughput sequencing of RNAs isolated by cross-linking immunoprecipitation [56] showed
that 4% of AGO-mRNA tags mapped to long non coding RNAs (lncRNAs). LncRNAs are >200 bases
long with low or no protein coding potential. These RNAs often regulate epigenetic silencing of genes
through chromatin remodeling. Several lines of evidences suggest that lncRNA expression levels may
undergo miRNA-guided regulation into the nucleus. In this view, specific AGO-miRNA complexes
seem able to target miRNA-complementary sequences within lncRNA affecting their stability and
function [57–61]. Thus, these results reveal a possible new nuclear function of miRNAs: miRNAs might
contribute to the regulation of the non-coding RNA transcriptome.
5.2. Nucleolar Function
miRNAs have been found to be significantly concentrated in the nucleolus as both pre-miRNAs
and mature miRNAs [62,63]. Various hypotheses have been proposed in order to describe possible
biological functions of nucleolar miRNAs [63,64]. For instance, the fact that miR-206 co-localizes with
28S ribosomal RNA (rRNA), both in the nucleolus and the cytoplasm in mammalian cells, may suggest
that miRNA can associate with ribosome subunits at an early stage of ribosome biogenesis [65].
As shown by Atwood et al. [66], minimal RISC (AGO2 and miRNA) may affect rRNA abundance in
cells. Moreover, the binding of minimal RISC to the 45S rRNA seems to be sensitive to Dicer knockdown
and actinomycin D treatment suggesting that tethering of AGO2 on rRNA depends on the presence
of miRNAs and at the same time requires an ongoing Pol I activity. Based on these findings, it is
possible to speculate that miRNA-targeted rRNAs may confer onto the mature ribosomes some specific
properties that help to define their interaction with accessory proteins. Reyes-Gutierrez et al. [67] have
also proposed that miRNAs bind to some mRNA targets in the nucleolus before their export to the
cytoplasm where mRNAs arrive in a pre-silenced status. Alternatively, nucleoli may constitute the
site of storage for miRNAs, which are redistributed into the nucleoplasm and/or cytoplasm following
genotoxic stress [64], thus evoking the ancestral role of the RISC as a genome defence system.
Furthermore, it has been suggested that pri- and pre-miRNAs may be A-to-I edited in the
nucleolus, as several RNA editing enzymes, such as the adenosine deaminases (ADARs), accumulate
in the nucleolus. This modification would inhibit maturation of miRNAs and thus reduce the cellular
availability of mature miRNAs [68], even though no edited miRNAs have been identified in the pool
of nucleolar miRNA to date [62,65,69,70]. All together, the above-mentioned models connect miRNAs
with nucleoli and indicate that nucleolar compartmentalization of miRNAs is required to affect mRNA
post-transcriptional regulation in the cytoplasm. Thus, dynamic movement of miRNAs to and from
the nucleolus is part of the program of mRNA regulation, which ultimately ends in the cytoplasm.
5.3. Regulation of Alternative Splicing
An emerging idea is of a hypothetical coordination between miRNA-mediated gene control and
splicing events in gene regulatory networks. Several studies have suggested that maturation of specific
miRNAs may depend on splicing factors [71,72]. Immunoprecipitation assays for nuclear AGO1 and
AGO2 proteins have highlighted their interaction with core components of the splicing machinery
and several splicing factors [73] underlining the interdependence between the two pathways. In order
to define both nuclear AGO2 and miRNA target sites on a transcriptome-wide scale, crosslinking
immunoprecipitation assays coupled with high throughput sequencing (HITS-CLIP) analyses have
been used. Through these assays, AGO2 and miRNA binding sites were identified within intronic
sequences, at a frequency ranging from 12%–15% in brain samples of mouse and human, respectively,

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and up to 3% in human myocardial cells [56,74,75]. These results constitute an important starting point
to support the idea of miRNA involvement in the cellular splicing program. However, it cannot be
excluded at this time that the isolated sequences represent retained intronic tracts targeted by RISC in
the cytoplasm [74]. Future work will be necessary to answer this question as well as to identify specific
miRNAs able to modulate alternative splicing.
Functional studies have in fact demonstrated the capability of AGO proteins to redirect splicing
only in association with exogenous small RNAs [76,77] or with endogenous small RNAs that are
different from miRNAs [73]. Data obtained from these studies are not in complete agreement and depict
two possible modes of action to explain miRISC participation to splicing modulation. Alló et al. [76]
revealed that small duplex RNAs, targeting both intronic and exonic sequences, near alternative
exons, could favor the inclusion of the variant exon. This process, dependent on AGO1, is associated
with an increase in H3K9me2 and H3K27me3 and is sensitive to Heterochromatin Protein 1 (HP1)
knockdown, suggesting a modus operandi of miRISC similar to that proposed for miRNA-guided
transcriptional gene silencing. More recently, Alló et al. [78] also found that ~80% of nuclear AGO1
clusters associate with transcriptional and non-transcriptional enhancers and thus influence alternative
and constitutive splicing more than transcription of the neighbouring genes. Similar conclusions were
reached by Ameyas-Zazoua et al. [73]. They showed that AGO1 and AGO2 are required to induce
remodelling of chromatin structure and splicing efficiency. To evaluate the impact of endogenous small
RNA depletion on alternative splicing events, both Alló and Ameryas-Zazoua groups have tested
the effect of Dicer knockout on splicing outcome. Data suggest that Dicer-dependent small RNAs,
such as endogenous small RNAs and miRNAs, are required to maintain the cellular splicing pattern.
Moreover, the two studies are in agreement in proposing an antisense transcript, rather than pre-mRNA,
as RISC-mediated splicing control target. In contrast, Liu et al. [77,79] have suggested that both
duplexes, RNA molecules and single stranded RNAs complementary to sequences near exon/intron
junctions, may modulate splicing by leading AGO2 to pre-mRNAs. These small oligonucleotides
would induce exon skipping in a chromatin modification independent manner. The proposed model
means that RISC binds the nascent transcript and thus impairs recruitment of the spliceosomal complex
to the splice junctions without affecting pre-mRNA transcription levels and stability.
5.4. Transcriptional Role of miRNAs
We know that siRNAs can regulate gene transcription [80], thus derogating from the most
consolidated activity of RNA interference. The fact that miRNAs possess a size comparable to that
of siRNAs, together with the idea that miRNAs and RISC elements are present in the nucleus, led to
examination of their ability to regulate gene expression at the transcriptional level. An important
number of studies have shown that miRNAs may mediate transcriptional gene activation (TGA)
or transcriptional gene silencing (TGS), thereby broadening the spectrum of activities of miRNAs
and revealing that miRNAs may function not only at the post-transcriptional level. The first miRNA
identified as an activator of gene transcription (TGA) was human miR-373, which induced transcription
of both E-cadherin (CDH1) and cold-shock domain-containing protein 2 (CSDC2) [81]. A discrete
number of reports have subsequently confirmed this observation. Other miRNAs have also been
identified as activators of gene transcription suggesting the existence of a new and widespread
mechanism of miRNA guided gene expression regulation [82–87]. These studies have led to the
identification of the conditions required for miRNA guided TGA but not the biochemistry of this
process or the relationship between protein effectors. A requirement for TGA is the presence in gene
promoters, of a DNA sequence complementary to the 5 -seed region in the miRNA and partially to
the flanking region. However, whether full or partial complementarity of the seed region is a strong
determinant for TGA remains unclear.
Recruitment of AGO proteins (mainly AGO2) [83] and RNApolII enrichment [83,85] at the
regulated gene promoters as well as modification of chromatin marks (increase of activator marks as
H3K4me3) accompany miRNA TGA [83]. As previously mentioned, several components of miRISC

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have been identified in the human nucleus. Furthermore, a miRISC does exist in the nucleus and
is characterized by a diverse complexity compared to the cytoplasmic one. AGO proteins, Dicer1,
TARBP2 and Gw182/TNRC6, have been identified in the nucleus and seem essential for mediating
transcriptional roles of miRNAs [36,37,39,40,88–91]. Although the mechanism or sequence of events
by which miRNAs induce TGA, are far from completely understood, several hypotheses have been
proposed based on the available data. One possible mechanism lies in the observation of the pervasion
of bidirectional transcription in the human genome. The human genome is transcribed in the both sense
and antisense directions [92–95]. Although the role of bidirectional transcription is not clear, we know
that it originates in non-coding antisense transcripts (mainly lncRNAs) overlapping sense promoters.
The role of these non-coding transcripts would be to repress the transcription of adjacent genes by
recruitment of repressive complexes, which mainly consist of chromatin effectors and modifiers in
close proximity of targeted gene promoters. The recognition by the miRNA seed region of a perfectly
matching sequence within a non-coding promoter transcript would recruit a nuclear RISC and induce
cleavage of the antisense non-coding transcript, removal of chromatin effectors and derepression of the
corresponding sense transcription [96,97] (Figure 1A). An alternative mechanism is that the miRNA
seed sequence recognizes a complementary sequence in the 5 UTR promoter region of a nascent RNA
or in a non-coding promoter transcript (pRNA). In this case, the minimal miRISC (AGO-miR) would
recruit a protein complex to a gene promoter region, consisting of proteins and activating chromatin
modifiers able to shift the chromatin structure toward a more permissive arrangement and thereby
increase gene transcription levels [85] (Figure 1B). This recruitment hypothesis is supported by the
observation that miRNA TGA is independent of target RNA cleavage [85].
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by which miRNAs induce TGA, are far from completely understood, several hypotheses have been
proposed based on the available data. One possible mechanism lies in the observation of the
pervasion of bidirectional transcription in the human genome. The human genome is transcribed in
the both sense and antisense directions [92–95]. Although the role of bidirectional transcription is not
clear, we know that it originates in non-coding antisense transcripts (mainly lncRNAs) overlapping
sense promoters. The role of these non-coding transcripts would be to repress the transcription of
adjacent genes by recruitment of repressive complexes, which mainly consist of chromatin effectors
and modifiers in close proximity of targeted gene promoters. The recognition by the miRNA seed
region of a perfectly matching sequence within a non-coding promoter transcript would recruit a
nuclear RISC and induce cleavage of the antisense non-coding transcript, removal of chromatin
effectors and derepression of the corresponding sense transcription [96,97] (Figure 1A). An
alternative mechanism is that the miRNA seed sequence recognizes a complementary sequence in
the 5′ UTR promoter region of a nascent RNA or in a non-coding promoter transcript (pRNA). In this
case, the minimal miRISC (AGO-miR) would recruit a protein complex to a gene promoter region,
consisting of proteins and activating chromatin modifiers able to shift the chromatin structure toward
a more permissive arrangement and thereby increase gene transcription levels [85] (Figure 1B). This
recruitment hypothesis is supported by the observation that miRNA TGA is independent of target
RNA cleavage [85].
Figure 1. Examples of alternative mechanisms of miRNA guided transcriptional gene activation
(TGA). (A) Long non coding RNAs (lncRNAs) or promoter associated RNAs (pRNAs) can silence
gene expression by recruiting a transcriptional repressive complex. miRNAs targeting a
complementary sequence within the lncRNA or pRNA would recruit a nuclear RISC and induce
cleavage of the antisense lncRNA or pRNA transcript promoting exclusion of repressive complex and
derepression of the sense transcription; (B) Alternatively, miRNAs induce gene activation by
recruiting a protein complex consisting of transcriptional activators. TNRC6A, Trinucleotide repeat-
containing 6A; TRBP, trans-activation response RNA-binding protein; AGO, Argonaute; TF,
Transcription Factor.
On the other hand, miRNAs have also been found to induce TGS. The first report describing miRNA
induced TGS was by Kim et al. [98]. Kim et al. described the transcriptional silencing activity of miR-320.
This miRNA, encoded within the promoter region of the POLR3D gene in the antisense orientation,
directed POLR3D transcriptional inhibition through recruitment of AGO1, Polycomb group (PcG)
component EZH2 and chromatin changes as observed in tri-methyl histone H3 lysine 27 (H3K27me3)
repressive mark enrichment. Numerous other examples of miRNAs inhibiting transcription of a single
Figure 1. Examples of alternative mechanisms of miRNA guided transcriptional gene activation
(TGA). (A) Long non coding RNAs (lncRNAs) or promoter associated RNAs (pRNAs) can silence gene
expression by recruiting a transcriptional repressive complex. miRNAs targeting a complementary
sequence within the lncRNA or pRNA would recruit a nuclear RISC and induce cleavage of the
antisense lncRNA or pRNA transcript promoting exclusion of repressive complex and derepression of
the sense transcription; (B) Alternatively, miRNAs induce gene activation by recruiting a protein
complex consisting of transcriptional activators. TNRC6A, Trinucleotide repeat-containing 6A;
TRBP, trans-activation response RNA-binding protein; AGO, Argonaute; TF, Transcription Factor.
On the other hand, miRNAs have also been found to induce TGS. The first report describing
miRNA induced TGS was by Kim et al. [98]. Kim et al. described the transcriptional silencing
activity of miR-320. This miRNA, encoded within the promoter region of the POLR3D gene in the
antisense orientation, directed POLR3D transcriptional inhibition through recruitment of AGO1,
Polycomb group (PcG) component EZH2 and chromatin changes as observed in tri-methyl histone H3

Int. J. Mol. Sci. 2016, 17, 1712 8 of 17
lysine 27 (H3K27me3) repressive mark enrichment. Numerous other examples of miRNAs inhibiting
transcription of a single gene or of small group of genes have subsequently been reported [99–102].
In addition, we and other authors have shown that miRNA driven transcriptional repression may affect
general cellular activities, such as senescence, nerve regeneration and granulopoiesis [91,103,104].
It is surprising that both activities (TGA and TGS) require similar features, components and
effectors, suggesting that these two apparently opposing biological events are tightly functionally
related. For instance, it is in general agreement that miRNA TGS requires the existence of
promoter-overlapping antisense transcription, the presence of miRNA seed-matches in the antisense
transcribed strand, and recruitment of AGO1 and/or AGO2 protein at the gene promoter, but differs
from TGA in the release of RNAPolII. In TGS, epigenetic modifications have a more prominent
role than in TGA. Recruitment of PcG proteins, modification of H3K27me3 (increase) and H3K4me3
(decrease) levels, and DNA methylation are frequently observed at miRNA regulated promoter regions.
Although the protein effectors of miRNA TGS have been identified, the nature of the recognition
mechanism and interaction between miRNAs and targeted promoters remains unclear. A number
of studies suggest a direct interaction between the miRNA seed sequence and the complementary
sequence in the transcribed strand, mainly in the antisense orientation, of the promoter overlapping
the promoter itself. In this view, the miRNA-targeted non-coding promoter associated RNA (pRNA)
would represent a docking platform for a protein inhibitory complex consisting of elements from the
RISC (AGO and Dicer1 proteins), PcG elements (YY1, EZH2 and SUZ12), and chromatin modifiers.
This interaction would enable a protein inhibitor complex to be in close proximity of the targeted
promoter region, the chromatin structure of which would be modified to establish a non-permissive
transcriptional status (Figure 2A). This model is based on the evidence from transcriptome studies
revealing that over 70% of gene promoters are overlapped by non-coding RNA transcripts [105] and
that gene promoter sequences are enriched with potential miRNA target sites [106] in both sense and
antisense orientations. Experimental procedures using synthetic gapmers or siRNA approaches to
inactivate pRNA function support results from the genomic analysis [89,95–97].
Int. J. Mol. Sci. 2016, 17, 1712 8 of 16
gene or of small group of genes have subsequently been reported [99–102]. In addition, we and other
authors have shown that miRNA driven transcriptional repression may affect general cellular activities,
such as senescence, nerve regeneration and granulopoiesis [91,103,104].
It is surprising that both activities (TGA and TGS) require similar features, components and
effectors, suggesting that these two apparently opposing biological events are tightly functionally
related. For instance, it is in general agreement that miRNA TGS requires the existence of promoter-
overlapping antisense transcription, the presence of miRNA seed-matches in the antisense transcribed
strand, and recruitment of AGO1 and/or AGO2 protein at the gene promoter, but differs from TGA in
the release of RNAPolII. In TGS, epigenetic modifications have a more prominent role than in TGA.
Recruitment of PcG proteins, modification of H3K27me3 (increase) and H3K4me3 (decrease) levels, and
DNA methylation are frequently observed at miRNA regulated promoter regions. Although the protein
effectors of miRNA TGS have been identified, the nature of the recognition mechanism and interaction
between miRNAs and targeted promoters remains unclear. A number of studies suggest a direct
interaction between the miRNA seed sequence and the complementary sequence in the transcribed
strand, mainly in the antisense orientation, of the promoter overlapping the promoter itself. In this view,
the miRNA-targeted non-coding promoter associated RNA (pRNA) would represent a docking platform
for a protein inhibitory complex consisting of elements from the RISC (AGO and Dicer1 proteins), PcG
elements (YY1, EZH2 and SUZ12), and chromatin modifiers. This interaction would enable a protein
inhibitor complex to be in close proximity of the targeted promoter region, the chromatin structure of
which would be modified to establish a non-permissive transcriptional status (Figure 2A). This model is
based on the evidence from transcriptome studies revealing that over 70% of gene promoters are
overlapped by non-coding RNA transcripts [105] and that gene promoter sequences are enriched with
potential miRNA target sites [106] in both sense and antisense orientations. Experimental procedures
using synthetic gapmers or siRNA approaches to inactivate pRNA function support results from the
genomic analysis [89,95–97].
Figure 2. Examples of alternative mechanisms of miRNA guided transcriptional gene silencing (TGS).
miRNAs can inhibit gene expression at transcriptional level. (A) In this case, miRNA-targeted non-
coding promoter associated RNA would represent a docking platform for a protein inhibitory
complex consisting of elements of RISC, PcG proteins and chromatin modulators. This interaction
would enable a protein inhibitor complex to be in close proximity of the targeted promoter region,
the chromatin structure of which would be modified to establish a non-permissive transcriptional
status; (B) Alternatively, miRNA guided recognition and interaction with promoter regions may
occur through a direct interaction between RNA and single-stranded DNA complementary
sequences. DNMTs, DNA methyltransferases; HDAC, Histone deacetylase; AGO, Argonaute; EZH2,
Enhancer of zeste homolog 2; Transcriptional Factor, TF; RNA Polymerase II, RNApolII.
Figure 2. Examples of alternative mechanisms of miRNA guided transcriptional gene silencing
(TGS). miRNAs can inhibit gene expression at transcriptional level. (A) In this case, miRNA-targeted
non-coding promoter associated RNA would represent a docking platform for a protein inhibitory
complex consisting of elements of RISC, PcG proteins and chromatin modulators. This interaction
would enable a protein inhibitor complex to be in close proximity of the targeted promoter region,
the chromatin structure of which would be modified to establish a non-permissive transcriptional
status; (B) Alternatively, miRNA guided recognition and interaction with promoter regions may
occur through a direct interaction between RNA and single-stranded DNA complementary sequences.
DNMTs, DNA methyltransferases; HDAC, Histone deacetylase; AGO, Argonaute; EZH2, Enhancer of
zeste homolog 2; Transcriptional Factor, TF; RNA Polymerase II, RNApolII.

Int. J. Mol. Sci. 2016, 17, 1712 9 of 17
However, it is well known that small RNAs are capable of hybridizing not only with other
RNAs, but also with double-stranded DNA to form relatively stable RNA*DNA:DNA triplexes via
Hoogsteen or reversed Hoogsteen base-pairing [107–110]. Therefore, alternative mechanisms of
miRNA directed TGS should be investigated and taken into consideration. The first evidence of
transcriptional regulation via the formation of a RNA*DNA:DNA triplex structure derives from the
observations of Martianov et al. [111]. These investigators observed RNA-dependent repression of
the major dihydrofolate reductase gene (DHFR) by a non-coding regulatory transcript transcribed
from the upstream minor promoter of this gene. This non-coding RNA induced promoter-specific
transcriptional repression through the disruption of the formation of the pre-initiation complex at
the major DHFR promoter. In order to demonstrate specificity of the RNA-dependent repression,
Martianov et al. [111] investigated the properties of the major DHFR promoter. This promoter was
found to be rich in GC content and contained several G-track sequences. Such sequences had been
previously shown to form stable purine-purine-pyrimidine triplex structures (H form) between DNA
and RNA. Thus, they analyzed the formation of the stable triplex structure between the major DHFR
promoter and the regulatory transcript. A standard H-form band-shift assay revealed the formation
of a specific DNA–RNA complex. Interestingly, a small synthetic oligoribonucleotide, corresponding
to the core of the major promoter, recapitulated the effects of the regulatory transcript and formed
a stable H form with promoter DNA, suggesting that small RNAs (such as miRNAs) have the potential
to target double stranded DNA.
The existence of transcription-regulating RNA*DNA:DNA structures is further supported by
work performed by Schmitz et al. on the mechanism of transcriptional repression of silent rRNA
genes [112]. These rRNA genes are silenced by NoRC, which requires association with pRNA for
its function. This pRNA originates from an RNA polymerase I promoter located upstream of the
pre-rRNA transcription start site. NoRC function depends on the interaction with the hairpin-forming
sequence of the pRNA. However, ectopically expressed pRNA lacking this sequence was able to induce
DNA hypermethylation and gene silencing as well as the full-length pRNA. Ectopic expression of
different truncated forms of pRNA revealed that transcriptional repression was induced as long as
the RNA sequence matching the T0 site (the binding site for the transcription factor TTF-1) on rDNA
was conserved. Thus, a stretch of 20-nt matching the T0 DNA sequence was sufficient to guarantee
the transcriptional repression of silent rRNA genes. In addition, in in vitro mobility shift and DNA
protection assays, the possible formation of a triplex structure formed by small stretch of 20-nt
in the pRNA and the T0 DNA sequence was observed. These studies along with the observation
that triple-helix target sites were found to be overrepresented at human gene promoters [113,114],
provide innovative insights depicting alternative mechanisms of action of small ncRNA (including
miRNAs) in TGS. However, the in vivo existence of RNA*DNA:DNA triplexes and their role still need
to be validated.
Alternatively, the observation that small RNAs can interact directly with the double-stranded
promoter DNA yields a second possibility, that RNA guided recognition and interaction with promoter
regions may occur through a direct interaction between RNA and single-stranded DNA complementary
sequences. This view was proposed by Jacob and Monod who argued that base complementarity would
enable RNA to interact specifically with other nucleic acid sequences in order to establish and transmit
diverse activities, including transcriptional activation, inhibition, recruitment of protein effectors,
and chromatin modification, at specific loci. Some experimental data substantiates a model based on
the recognition and direct interaction between small RNAs and complementary DNA sequences at
gene promoters. Regarding TGA, Zhang et al. [113] have reported that some cellular miRNAs in human
peripheral blood mononuclear cells associate with RNApolII and the TATA binding protein. They also
were found to bind directly to TATA box motifs at gene promoters, inducing transcription of the
target gene. In addition, Nakama et al. [114], through RNA immunoprecipitation assays, showed that
an ncRNA, transcribed from both strands of centromeric dh repeats in fission yeast, was associated
with chromatin through the formation of a DNA-RNA hybrid. The presence of DNA-RNA hybrids

Int. J. Mol. Sci. 2016, 17, 1712 10 of 17
in the cell was confirmed by immunofluorescence analysis with an anti-DNA-RNA hybrid antibody.
Overexpression or depletion of RNase H in in vivo experiments led to decreased and increased
levels, respectively, in the amount of the DNA-RNA hybrid that formed, and in both experiments,
heterochromatin changes were induced.
Important assessments can also be made from studies specifically evaluating the mechanism of
miRNA guided TGS. For instance, we demonstrated that miR-223 drives TGS of NFI-A through
two DNA sequences within the NFI-A promoter region complementary to the miR-223 seed
sequence [91]. We demonstrated through multiple approaches that during human granulopoiesis,
miR-223 entered the nucleus and localized at its complementary sequences on the NFI-A promoter.
These approaches included confocal microscopy of transfected fluorescent miR-mimics and in situ
hybridization to the endogenous miRNA with fluorescent oligonucleotides complementary to the
sequence of miR-223. We also detected miR-223-specific signals on mitotic chromosomal spreads from
cells undergoing myeloid differentiation. These signals were detectable on symmetrical regions
of sister chromatids, suggesting a gene-specific localization. Since, RNA synthesis is blocked
during metaphase, this finding may support a view whereby miR-223 directly binds to DNA on
specific sequences. By combining transfection of a Cy5-labeled miR-223 with anti-Cy5 chromatin
immunoprecipitation, we were able to demonstrate that miR-223 does interact with the NFI-A promoter
DNA. Here, miR-223 is part of a ribonucleoprotein repressive complex involving YY1, Dicer1 and
AGO1. The localization of this complex on the NFIA promoter was RNA-dependent, since it was
prevented by RNase H which specifically recognizes RNA:DNA hybrids. In addition, in experiments
with stable cell lines engineered to express a promoter-luciferase cassette including ~1.4 kb of the NFI-A
promoter, the integrity of the two miR-223 DNA sequences complementary to the miR-223 seed was
found to be necessary for transcriptional inhibition. Our data suggest that miR-223-mediated TGS may
occur by a mechanism that does not rely on antisense transcription, as it does not occur when reporter
constructs are used. Based on our observations, however, we instead prefer a mechanism that requires
an RNA:DNA interaction (Figure 2B). In addition, although Martianov et al. [111] favor a model based
on antisense-promoter-transcription guidance, they cannot exclude a direct interaction between RNA
and DNA to explain RNA-dependent repression of DHFR. In a similar manner, Adilakshmi et al. [104]
suggested that miR-709 exerted its effect by binding in trans and regulating the antisense strand of
the EGR2 promoter because the Myelin specific element (MSE) exhibits miRNA binding sites in both
strands. However, the same authors also state “It is beyond doubt however, that miR-709 interacts
directly with the MSE-promoter DNA as indicated by the susceptibility of the complex to RNase
H treatment”. More revealing, are data generated by Miao et al. [102] demonstrating that miR-552
transcriptional repression was mediated by the binding, through its non-seed sequence, to a hairpin
loop in the DNA cruciform structure in the CYP2E1 promoter region.
6. Conclusions
Taken together, these data demonstrate that there is tremendous versatility in miRNA function.
miRNAs have clear roles in both the cytoplasm and nucleus where they have been found to
regulate gene expression through different mechanisms. In the nucleus (Figure 3), emerging data
implicates miRNAs in the regulation of the stability of mRNA in nucleoli and alternative splicing.
More compelling data points to direct involvement in the regulation of gene expression at the
transcriptional level. Here, miRNAs may mediate both activation and inhibition of transcription
of a target gene. Both of these biological processes appear to be dependent on the presence of a DNA
promoter sequence complementary to the seed region of a regulatory miRNA and on a non-coding
transcript overlapping the gene promoter itself. The recognition between the miRNA and the
complementary sequence on the non-coding RNA occurs through classic Watson and Crick base
pairing. Although this model is currently the most widely favored, there is data suggesting that miRNA
guided recognition and interaction with promoter regions may occur through a direct interaction
between RNA and single-stranded DNA complementary sequences. More evidence is needed to

Int. J. Mol. Sci. 2016, 17, 1712 11 of 17
support this mechanism of action of miRNAs in vivo, but this alternative model is attractive because of
its simplicity and high specificity. miRNAs therefore might bind directly and specifically to promoter
DNA, just as transcription factors, and serve as a platform for the localization of transcriptional
regulators and chromatin modifying proteins at genomic loci.
The versatility and complexity of mechanisms by which miRNAs regulate gene expression,
at cytoplasmic and nuclear level, imply that alteration of miRNAs regulatory mechanisms may affect
normal cellular functions. The alteration of miRNAs biogenesis mechanism, miRNAs expression level
and miRNAs regulatory networks affects important biological pathways such as cellular differentiation
and apoptosis and it is detected in various human diseases and syndromes, especially in cancer
(for a review see Ghai and Wang [115]). All tumors present specific signatures of miRNAs altered
expression. For this reason, miRNAs expression profiles of tumors may represent valid and useful
biomarkers for diagnosis, prognosis, patient stratification, definition of risk groups and to monitor
the response to therapy. In most cases these profiles are obtained from biopsy material. The biggest
advantage of using miRNAs is that they are released from the tumor tissue in the plasma where they
can be easily collected and analyzed, especially if embedded in extracellular vesicles [115]. To date
miRNAs represent the most promising class of molecular biomarkers. Equally relevant is the emerging
role of microRNAs in viral infections. Data from literature show a mutual interference between viruses
and the host cell’s miRNA machinery. For instance, viruses may impair the host cell’s miRNA pathway
by interacting with specific proteins; synthesize their own miRNAs to modify cellular environment
or to regulate their own mRNAs; or make use of cellular miRNAs to their favor. However, it is also
true that host cell’s miRNAs may target viral mRNAs. In many cases, this bidirectional interference is
resolved in favor of the viruses that as a result may escape the immune response and complete the
replication cycle (for a review see Verma et al [116] and Piedade and Azevedo-Pereira [117]).
Int. J. Mol. Sci. 2016, 17, 1712 11 of 16
The versatility and complexity of mechanisms by which miRNAs regulate gene expression, at
cytoplasmic and nuclear level, imply that alteration of miRNAs regulatory mechanisms may affect
normal cellular functions. The alteration of miRNAs biogenesis mechanism, miRNAs expression level
and miRNAs regulatory networks affects important biological pathways such as cellular differentiation
and apoptosis and it is detected in various human diseases and syndromes, especially in cancer (for a
review see Ghai and Wang [115]). All tumors present specific signatures of miRNAs altered expression.
For this reason, miRNAs expression profiles of tumors may represent valid and useful biomarkers for
diagnosis, prognosis, patient stratification, definition of risk groups and to monitor the response to
therapy. In most cases these profiles are obtained from biopsy material. The biggest advantage of using
miRNAs is that they are released from the tumor tissue in the plasma where they can be easily collected
and analyzed, especially if embedded in extracellular vesicles [115]. To date miRNAs represent the most
promising class of molecular biomarkers. Equally relevant is the emerging role of microRNAs in viral
infections. Data from literature show a mutual interference between viruses and the host cell’s miRNA
machinery. For instance, viruses may impair the host cell’s miRNA pathway by interacting with specific
proteins; synthesize their own miRNAs to modify cellular environment or to regulate their own
mRNAs; or make use of cellular miRNAs to their favor. However, it is also true that host cell’s miRNAs
may target viral mRNAs. In many cases, this bidirectional interference is resolved in favor of the viruses
that as a result may escape the immune response and complete the replication cycle (for a review see
Verma et al [116] and Piedade and Azevedo-Pereira [117]).
Figure 3. Schematic representation of the function of miRNAs in the nucleus. Nuclear miRNAs may
activate (TGA) or inhibit (TGS) gene transcription, block maturation of non-coding RNAs (LncRNA,
pri-miRNA, pre-miRNA), affect alternative splicing (orange arrow); more controversial is miRNAs
function in the nucleolus where they might affect maturation of ribosomal RNAs (rRNAs) and of
messenger RNA (mRNAs) (orange arrow). pri-miRNA, primary miRNA; pre-miRNA, precursor
miRNAs; miRISC, miRNA inducing silencing complex.
Conflicts of Interest: The authors declare no conflict of interest.
References
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microRNAs. Genome Res. 2009, 19, 92–105.
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precursor miRNAs; miRISC, miRNA inducing silencing complex.
Conflicts of Interest: The authors declare no conflict of interest.
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© 2016 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access
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