REVIEW
Control of cytoplasmic mRNA localization
Karen Shahbabian • Pascal Chartrand
Received: 25 May 2011 / Revised: 9 August 2011 / Accepted: 1 September 2011 / Published online: 8 October 2011
Ó Springer Basel AG 2011
Abstract mRNA localization is a mechanism used by
various organisms to control the spatial and temporal
production of proteins. This process is a highly regulated
event that requires multiple cis- and trans-acting elements
that mediate the accurate localization of target mRNAs.
The intrinsic nature of localization elements, together with
their interaction with different RNA-binding proteins,
establishes control mechanisms that can oversee the transcript
from its birth in the nucleus to its specific final
destination. In this review, we aim to summarize the different
mechanisms of mRNA localization, with a particular
focus on the various control mechanisms that affect the
localization of mRNAs in the cytoplasm.
Keywords Cytoplasmic RNA transport Á
RNA localization Á Localization elements Á
RNA-binding proteins
Introduction
The cytoplasmic transport and localization of mRNAs is a
post-transcriptional mechanism that restricts the synthesis
of proteins to specific sites within cells. For years, studies
on mRNA localization were limited to a few localized
transcripts in a small number of model systems. Now, this
process has been observed in several branches of the
eukaryotic tree, from fungi to mammals and plants [1–3].
Recent evidence even points to translation-independent
mRNA localization in eubacteria [4]. Moreover, in the past
few years, large scale screens based on biochemical,
genomic, or cytological assays identified subpopulations of
mRNAs that are localized to several subcellular domains or
organelles, such as the endoplasmic reticulum [5], mitochondria
[6], the bud of yeast cells [7], Drosophila
blastoderm embryo [8], the mitotic microtubules [9],
dendrites [10], axons [11, 12], and pseudopodia [13]. These
studies revealed that mRNA localization is more widespread
and involves a larger set of transcripts than
previously thought. Typical examples of mRNA localization
are presented in Fig. 1.
Why do cells use this mechanism to regulate gene
expression? One reason is that mRNA localization limits
the expression of a protein to a specific time and place.
Indeed, several localized mRNAs encode proteins involved
in asymmetric cell division or cell fate determination,
which requires a delicate spatiotemporal regulation of these
factors [14]. This mechanism also facilitates protein sorting
to organelles, as several mRNAs coding for mitochondrial,
endoplasmic reticulum (ER), and even peroxisome proteins
are enriched at these organelles [15, 16]. Another function
of mRNA localization is to restrict the expression of
potentially toxic proteins. A good example is the mRNA of
myelin basic protein MBP, which is localized to myelinating
oligodendrocyte processes [17]. Disruption in the
localization of MBP mRNA leads to ectopic MBP
expression and aberrant myelination in vivo [18].
In this article, we review the main mechanisms of
mRNA localization with a special focus on the different
levels of control of the localization of mRNAs. We will
pay attention to three levels of control: (1) the nuclear
events leading to the recognition of localized transcripts by
their localization factors, (2) the role of cis-acting elements
in modulating mRNA localization, and (3) the extracellular
signaling pathways that regulate mRNA localization.
K. Shahbabian Á P. Chartrand (&)
Department of Biochemistry, Universite´ de Montre´al,
2900 Edouard-Montpetit, Montre´al, Qc, Canada
e-mail: p.chartrand@umontreal.ca
Cell. Mol. Life Sci. (2012) 69:535–552
DOI 10.1007/s00018-011-0814-3 Cellular and Molecular Life Sciences
123
We will not cover the translational control of localized
mRNA since excellent reviews on this subject have been
published recently [19–21].
Mechanisms of mRNA localization
For several transcripts, their localization depends on the
presence of a peptide sequence in the emerging peptidic
chain that targets the translated mRNA to its site of
localization. This mechanism has been well described for
transcripts encoding secreted or membrane proteins that are
localized to the ER, for instance [22]. Nevertheless, a large
number of transcripts do not depend on translation for their
localization, as they are frequently transported in a translationally
repressed form. A common theme for these
localized mRNAs is that they contain cis-acting elements
in their sequences, called zipcodes or localization elements,
which are recognized by specific trans-acting RNA-binding
proteins [23]. These localization elements are
commonly found in the 30
untranslated region (UTR) of
transcripts [23]. However, in several cases, localization
elements have been identified in the 50
UTR or coding
region of mRNAs [24, 25]. The RNA-binding proteins
associated with a transcript determine the mechanism used
for its localization.
Diffusion and entrapment of mRNA
One of the simplest ways to localize an mRNA is for the
transcript to diffuse in the cytoplasm and then become
trapped at a specific location via binding to anchors. During
late stages of oogenesis in Drosophila, Nanos is localized at
the posterior pole of embryos, where it acts as a translational
repressor of hunchback mRNA, thereby allowing
expression of genes involved in abdominal development
[26]. Posterior localization of this protein is also essential
for germ cell development [27]. However, only 4% of total
nanos mRNA is localized at the posterior and the rest can be
found throughout the cytoplasm [28]. Live cell imaging
of endogenous nanos mRNA by GFP-tagging revealed
a motor-independent mechanism for localization of this
transcript at the oocyte posterior [29]. When oocytes are
treated with microtubule depolymerization agents, nanos
Fig. 1a–e Examples of
localized mRNAs.
a Localization of the ASH1
mRNA (red) at the bud tip of
the budding yeast
Saccharomyces cerevisiae (left
panel). Nuclear DNA is in blue.
Nomarski image is shown in the
right panel. Image taken from
[59]. b Localization of Vg1
localization element (VLE)
RNA (red) at the vegetal pole of
Xenopus oocyte. The image was
provided by James Gagnon and
Kim Mowry, Brown University.
c Localization of bicoid mRNA
(green) at the anterior pole of a
Drosophila embryo. Red DAPI.
d Localization of nanos mRNA
at the posterior pole of a
Drosophila embryo. Red DAPI.
The images were provided by
E´ric Le´cuyer, Institut de
Recherche Clinique de
Montre´al. e CamKIIa mRNA
granules (red) in dendrites of
cultured hippocampal neuron.
White square presents higher
magnification of RNA granules
in dendrites (showed in the
upper right panel). The image
was provided by Sharon
Swanger and Gary Bassell,
Emory University [189]
536 K. Shahbabian, P. Chartrand
123
mRNA can still localize to the posterior pole, but since
cytoplasmic streaming is reduced, less nanos mRNA gets to
the pole [29]. This suggests that nanos mRNA is localized
mainly by a diffusion-based mechanism. On the other hand,
while actin filaments are not involved in nanos mRNA
transport, they are necessary for its anchoring at the posterior
pole [29, 30].
Another well studied example of the diffusion-entrapment
mechanism is the Xenopus Xcat-2 mRNA, which
encodes a Nos related zinc-finger RNA-binding protein
[31]. During the early stages of Xenopus oogenesis, Xcat-2
mRNA is restricted to a specific structure in the cytoplasm
called the mitochondrial cloud (MC). The mitochondrial
cloud, also called Balbiani body, consists mostly of mitochondria
and small vesicles, and is the source of germinal
granule material [32]. The movement of the MC in the
cytoplasm results in the localization of the Xcat-2 mRNA
at the vegetal cortex. Transfer of this mRNA to the vegetal
pole is suggested to occur through a region of the MC
called the Message transport organizing center (METRO).
Xcat-2 mRNA accumulates within this region and subsequently
localizes to the vegetal cortex (Fig. 2a) [33, 34].
Direct evidence that supports the diffusion and entrapment
model for this mRNA came from a study in which the
authors used time-lapse confocal microscopy and FRAP
analysis to monitor the movement of injected fluorescent
Xcat-2 RNA construct. Upon injection, the Xcat-2 mRNA
diffuses into the cytoplasm and subsequently aggregates in
the METRO region of the MC [35]. This pathway is motorindependent
since depolymerization of the microtubules
has no effect on the localization of Xcat-2 in MC [35].
However, a recent study reported that Xcat-2 mRNA
localization during early stages of oogenesis is reduced by
inhibition of Kinesin II, suggesting that the migration of
Xcat-2 mRNA to the MC depends to some extent on this
molecular motor [36]. Finally, anchoring of the Xcat-2
transcript upon arrival to the MC is suggested to occur via
its association with a distinct domain of the ER in the MC
region and is independent of germinal granule formation
[35]. However, factors mediating this association still
remain to be determined.
Selective degradation and stabilization of mRNA
Localized stabilization of a transcript is another mechanism
by which an mRNA can be subcellularly targeted. In this
case, an mRNA is rapidly degraded in most parts of the
cell, but it is protected from degradation at a specific
location. The hsp83 mRNA, which encodes a heat shock
protein in Drosophila, is a well-characterized example of
this kind of localization (Fig. 2b). This transcript is localized
at the posterior pole of the early Drosophila embryo
by the selective stabilization of the mRNA at the posterior
pole and degradation of the transcript elsewhere in the
cytoplasm [37]. The level of hsp83 mRNA, which is a
maternally encoded transcript, decreases more rapidly in
embryos than in unfertilized eggs, which suggests that two
separate mechanisms control the stability of this transcript
[38]. These two independent pathways, which are called
‘‘maternal’’ and ‘‘zygotic’’ pathways, use maternally and
embryonic encoded proteins, respectively, to degrade the
hsp83 transcript [38]. By analyzing the 30
UTR of hsp83
mRNA, a region from nucleotides 253–349 was identified
as the Hsp83 degradation element (HDE), which directs the
destabilization of this mRNA in unfertilized eggs. However,
this region has no effect in the zygotic degradation
pathway, and transcripts without the HDE domain are
subject to degradation by the embryonic degradation
machinery [38]. The hsp83 ORF has also been shown to
affect the stability of the transcript. A region at the 30
end
of the ORF, which comprises 615 nucleotides, has been
found to be responsible for this destabilization, and was
consequently called Hsp38 instability element (HIE) [39].
This region, which has the major effect in the destabilization
of the transcript, functions together with the HDE
for complete degradation. The HIE domain contains six
stem-loop structures that are recognized by the maternally
encoded RNA-binding protein Smaug [39, 40]. It was
shown that in Smaug mutants, degradation and thus
localization of hsp83 mRNA are impaired. Smaug recruits
the CCR4/POP2/NOT deadenylase complex, triggering
deadenylation and thus degradation of the hsp83 transcript
[40]. Although Smaug is present throughout the pole
plasm, the hsp83 mRNA is protected from Smaug action at
the posterior pole. This protection is related to a 57 nt
region in the 30
UTR (nucleotides 351–407) downstream of
HDE, which is called HPE (Hsp83 protection element).
HPE is sufficient to confer stability to an unstable transcript
at the pole plasm [40]. The mechanism by which this
domain functions is not clear, and may include interaction
of trans-acting factors that block the availability of the
transcript to Smaug.
Smaug is involved in the degradation of several maternal
mRNAs in Drosophila, and its expression is regulated
by the PAN GU kinase (PNG), which controls smaug
mRNA translation [41]. Among the maternal transcripts
whose selective degradation by the Smaug/CCR4 complex
restricts their localization at the posterior pole is the nanos
mRNA. As mentioned in the previous section on diffusion
and entrapment of mRNA, only 4% of total nanos mRNA
is localized at the posterior pole, while the bulk of nanos
mRNA is distributed in the cytoplasm in a translationally
repressed complex and is actively degraded. Degradation
of nanos mRNA depends on the CCR4/NOT deadenylase
complex and is recruited on this transcript by Smaug [42].
Deadenylation of nanos mRNA by CCR4/NOT also
Control of cytoplasmic mRNA localization 537
123
contributes to the translational repression of this transcript.
Only a fraction of nanos mRNA is stabilized at the posterior
pole of the embryo, and this occurs via the action of
Oskar, which prevents the binding of Smaug to the nanos
mRNA [42]. However, Smaug is not the only activator of
nanos mRNA decay, and a recent study reported that the
piRNA pathway is also involved in nanos mRNA degradation
[43]. In Drosophila, piRNAs or Piwi-interacting
RNAs, are small RNAs of 22–30 nucleotides that are
abundant in the germ line and which mostly derive from
transposons or other repeated elements (reviewed in [44]).
These RNAs are associated with PIWI-types Argonaute
proteins such as Piwi, Aubergine, and Ago3, and they
participate in the silencing of transposons by directing the
cleavage of transposon transcripts. Simonelig and colleagues
found that mutants of factors involved in piRNAs
biogenesis (such as Armitage, Spindle-E, and Squash) or in
the Piwi-type Argonaute proteins Aubergine and Ago3,
which are associated with piRNAs, result in the stabilization
of nanos mRNA and ectopic expression of Nanos
protein throughout the embryo [43]. Deletion of putative
piRNA binding sites in the 30
UTR of nanos mRNA
increases the stability of this transcript and results in
embryo patterning defects. Interestingly, Aubergine, Ago3,
Smaug, CCR4, and nanos mRNA are present in the same
complex, suggesting that Smaug/CCR4 and the piRNA
pathway cooperate to regulate nanos mRNA deadenylation
and degradation.
Active transport
The motor-based transport of transcripts is used by most
cell types to actively localize mRNAs to specific cellular
subregions [45]. In the cytoplasm, the ribonucleoprotein
(RNP) complex associates with molecular motors that are
required for active transport along the cytoskeleton [46].
Microtubule-dependent motors, such as the minus-end
dynein or the plus-end kinesin motors, are commonly used
for the transport of mRNA over long distances, either in
fungi, Drosophila, Xenopus, or mammalian cells (see
examples below) [46, 47]. The non-canonical type V
myosin is also used as a molecular motor to carry transcripts
on the actin cytoskeleton, usually over short
distances (see examples below) [48, 49].
Nuclear events that control cytoplasmic mRNA
localization
It is well established that nuclear processing of nascent
mRNA affects its cytoplasmic fate by controlling different
mechanisms, including translation and degradation
[50]. The possibility that nuclear events also affect the
cytoplasmic localization of an mRNA emerged from the
finding that several RNA-binding proteins involved in
mRNA localization are either nuclear residents or shuttle
between the nucleus and the cytoplasm [51]. Indeed, several
lines of evidence now suggest that localized mRNAs
are ‘‘marked’’ in the nucleus prior to their export to the
cytoplasm. Different mechanisms leading to the ‘‘marking’’
of localized mRNAs in the nucleus have been uncovered in
the past few years.
Cotranscriptional recruitment of mRNA localization
factors
The observation that mRNAs can be ‘‘marked’’ for cytoplasmic
localization in the nucleus raises the possibility that
these events may occur on the nascent transcripts, during
transcription. The ZBP1 protein1
, which is involved in the
localization of b-actin mRNA to the leading edge of
chicken embryo fibroblasts, is predominately cytoplasmic,
but it shuttles between the nucleus and cytoplasm and is
recruited cotranscriptionally to the b-actin mRNA [52].
Another zipcode-binding protein, ZBP22
, is also involved in
b-actin mRNA localization [53]. ZBP2 is a predominately
nuclear protein, which is also recruited cotranscriptionally
to the nascent b-actin mRNA [54]. During b-actin mRNA
synthesis, ZBP2 binds to the zipcode before ZBP1, and its
binding favors ZBP1 recruitment. However, both proteins
recognize distinct but adjacent motifs of the b-actin zipcode.
It was suggested that upon ZBP1 binding, ZBP2
dissociates from the zipcode, thus the mRNA that leaves the
nucleus contains only ZBP1 [54]. This differential binding
of ZBP2 and ZBP1 therefore mediates the assembly of the
b-actin mRNA localization complex before its export to the
cytoplasm.
How important is the nuclear recognition of localized
mRNAs by their localization factors and to what extent
does the transcription machinery participate in this process?
Evidence from the budding yeast suggests that early
nuclear events are crucial to ultimately define the cytoplasmic
localization of a transcript. The yeast RNAbinding
protein She2 interacts directly with cis-acting
elements of bud-localized transcripts and directs them to
1
The ZBP1, Vg1 RBP/Vera, IMP1, 2, 3, CRD-BP, and KOC proteins
are part of the same family of RNA-binding proteins that contain two
RNA recognition motifs (RRM) followed by four hnRNP K
Homology (KH) domains. ZBP1 is the chicken ortholog of the
mammalian IGF-II RNA binding protein 1/IMP1, a member of a
family of three highly related paralogs, IMP1 to 3. Xenopus Vg1
RBP/Vera is the ortholog of mammalian IMP3.
2
ZBP2, KSRP, FBP1, 2, 3, and MARTA are part of the same family
of RNA-binding proteins that contain four KH domains. ZBP2 is the
chicken ortholog of FBP2, a member of the three mammalian
paralogs FBP1-3.
538 K. Shahbabian, P. Chartrand
123
the localization machinery [55, 56]. She2, unlike other
proteins of the locasome (i.e., the multiproteic complex
involved in the transport and targeting of bud localized
mRNAs in S. cerevisiae, see more details below), is present
in both the nucleus and cytoplasm. Indeed, it was shown
that She2 shuttles between the cytoplasm and nucleus, and
that nuclear export of She2 depends on binding to RNA,
suggesting that it recognizes its target mRNAs in the
nucleus [57]. She2 shuttling depends on a non-classical
nuclear localization signal (NLS) and mutations in this
motif lead to impaired localization of ASH1 mRNA to the
bud tip, suggesting that nuclear shuttling of She2p is
important for ASH1 mRNA sorting [58, 59]. Recently it
was shown that She2 interacts with the elongating RNA
polymerase II via the transcription elongation factor Spt4Spt5/DSIF
[60]. This interaction leads to the co-transcriptional
recruitment of She2 to bud-localized transcripts, and
mutants of SPT4 and SPT5 were found to display defective
ASH1 mRNA localization. This finding reveals an important
role for the transcription machinery in the very first
steps of localization events in the nucleus and shows that
the association of She2 with the transcription machinery
promotes the recruitment of this factor on nascent transcripts
[61].
Splicing and mRNA localization
Splicing of pre-mRNA is a mechanism for the excision of
introns from the protein-coding exonic sequences. A premRNA
can also give rise to different transcripts by alternative
splicing of its exons, coding for different variants of
a protein [62]. Splicing variants can result in the retention
or elimination of a localization element in an mRNA,
leading to various transcripts that can localize to different
parts of a cell. An example is the stardust A (sdt) mRNA,
which localizes at the apical pole of Drosophila follicle
cell epithelium, leading to the apical localization of the Sdt
protein, a regulator of the Crb complex [63]. Localization
of sdt mRNA is regulated during development and depends
on the alternative splicing of coding exon 3, which is
thought to contain a localization element [63]. While exon
3 is present during early oogenesis, leading to the localization
of sdt mRNA to the apical pole, exclusion of this
exon by alternative splicing at stage 10 results in unlocalized
sdt mRNA. Other localized mRNAs are known to be
regulated via alternative splicing of their localization elements,
such as the cyclin B mRNA in Drosophila [64].
Surprisingly, intronic sequences can also mediate mRNA
localization. Indeed, a recent study revealed that retention
of specific introns in neuronal transcripts could be involved
in their localization at dendrites [65]. These cytoplasmic
intron sequence-retaining transcripts (CIRTS) are present
in mammalian neurons and contain introns with short
interspersed repetitive elements (SINE) derived from the
BC1 RNA. These elements are thought to be responsible
for the localization of the non-coding BC1 RNA to dendrites
in rodents [66]. However, recent in vivo studies in
mice were unable to confirm the role of these elements in
dendritic mRNA localization [67].
The splicing reaction itself can be an important factor
for cytoplasmic localization of an mRNA. In metazoans,
splicing of pre-mRNA leaves a specific complex on
sequences located upstream of the exon–exon junction: the
exon junction complex (EJC). This complex is exported to
the cytoplasm with the mature mRNA and remains associated
until the first round of translation [68]. The EJC
plays an important role in mRNA export, translation, and
quality control [69]. Surprisingly, a role for the EJC in the
localization of oskar mRNA at the posterior pole of
Drosophila oocyte has also been uncovered. Indeed,
mutants of components of the EJC, such as eIF4AIII, Mago
Nashi, and Tsunagi/Y14 disrupt oskar mRNA localization
[70–72]. Interestingly, only the splicing of the first intron is
important for proper localization, as its deletion leads to
impaired localization at the posterior pole. However, oskar
transgenes in which the first intron was substituted by
another intron sequence still localized their mRNA normally,
suggesting that it is the position of the EJC complex
that is important for localization [70]. The mechanism by
which nuclear splicing is coupled to cytoplasmic localization
of oskar mRNA is probably via an interaction with
Barentz (Btz), a cytoplasmic protein essential for oskar
localization [73]. Btz interacts with eIF4AIII and is
subsequently recruited to the oskar mRNA localization
complex [74]. Since eIF4AIII is a general factor present in
the EJC of all spliced mRNAs, it is not clear how Btz
would recognize only the oskar mRNA.
Nuclear assembly of the mRNA localization complex
As mentioned above, some of the trans-acting factors
involved in mRNA localization shuttle between the nucleus
and the cytoplasm, suggesting that the mRNA localization
process is initiated in the nucleus. In Xenopus, the localization
of maternal transcripts such as the Vg1 and VegT
mRNAs to the vegetal pole of oocytes depends on a multiprotein
complex that contains the RNA-binding proteins
hnRNP I and the Xenopus homolog of ZBP1, the Vg1RBP/
Vera protein [75–77]. The vegetal localization of Vg1 is
mediated by localization elements in the 30
UTR of the
transcript [78]. The Vera protein recognizes and specifically
binds the localization elements of Vg1 and VegT
mRNAs in the oocytes and directs their localization via
formation of an mRNP complex [79, 80]. By analyzing
RNA–protein interactions of oocyte mRNP complexes,
Kress and colleagues [81] found that hnRNP I and Vera
Control of cytoplasmic mRNA localization 539
123
associate with Vg1 and VegT mRNAs in both the nucleus
and the cytoplasm, indicating that the very first step of
cytoplasmic localization of maternal mRNAs in the
oocytes starts in the nucleus. Upon nuclear export, additional
factors such as xStau, the Xenopus homolog of
Staufen, and Prrp are recruited to the mRNP complex and
direct their vegetal localization during mid-oogenesis [82,
83]. Moreover, nuclear RNA-binding proteins, such as the
yeast Loc1 protein [84] or the vertebrate ZBP2 protein
[53], bind and promote the cytoplasmic localization of
ASH1 and b-actin mRNA, respectively. This further supports
the idea of a nuclear ‘‘marking’’ of mRNAs destined
for a particular cytoplasmic localization.
Cis-acting localization elements and the control
of mRNA localization
Once in the cytoplasm, marked mRNAs are targeted for
their specific localization. As mentioned above, the presence
of a cis-acting localization element is essential for the
recognition and targeting of an mRNA via a specific
localization pathway. For some localized transcripts, the
presence of a single localization element is sufficient to
allow efficient localization [85]. However, the analysis of
localization elements in several transcripts revealed a more
complex picture, in which redundant or different localization
elements are required for optimal localization of an
mRNA.
Redundant localization elements can act cooperatively
to promote mRNA localization
Having several copies of the same localization element in
an mRNA is a way to ensure the efficient transport and
localization of a transcript and can be a consequence of the
type of molecular motor used for its transport. Indeed,
association with a poorly processive motor may require the
recruitment of several copies of this motor to a single
mRNA in order to maintain continuous transport. A good
example is the ASH1 mRNA in the budding yeast Saccharomyces
cerevisiae, which is localized at the bud tip
during late anaphase of the cell cycle [86, 87]. Localization
of ASH1 mRNA is essential for the asymmetric distribution
of Ash1, which acts as a transcriptional repressor of the HO
endonuclease and results in inhibition of mating-type
switching in daughter cells [88, 89]. The ASH1 mRNA
contains four localization elements, three in the coding
sequence (E1, E2A, and E2B) and one overlapping the end
of the coding sequence and the 30
UTR (E3) [25, 90]. While
the presence of these four elements leads to an optimal
localization, deletion analysis revealed that each element is
sufficient for localization of a reporter mRNA to the bud.
When each of these elements was inserted in multiple
copies in the 30
UTR, the new constructs showed nearly
normal localization. However, for these mRNAs, the
asymmetric distribution of Ash1 was impaired, suggesting
that the position of these elements is important for Ash1
sorting but not for ASH1 mRNA localization [91].
Although the primary sequences of the four ASH1 localization
elements are different, they all fold into a stem-loop
structure that contains a few conserved nucleotides
[92, 93]. All four elements interact with the same RNAbinding
protein called She2, which is involved in the
localization of bud-localized mRNAs in S. cerevisiae
[7, 55, 56]. She2 forms a tetramer under physiological
conditions, and mutations that disrupt this tetrameric state
abolish its RNA-binding capacity and impair She2-dependent
localization to the bud tip [94]. She2 interacts directly
with the C-terminal domain of She3, an adaptor protein
that links the She2–mRNA complex to the molecular motor
Myo4 (Fig. 2c) [55, 95, 96]. Recent evidence also suggests
that She3, besides its role in connecting the She2–RNA
complex to Myo4, is itself able to bind RNA and acts
synergistically with She2 to increase the affinity and
specificity of RNA binding [97].
Recent studies on Myo4 helped to explain why multiple
localization elements are required for proper ASH1 mRNA
localization. Myo4 is a class V myosin whose main function
is the transport of mRNAs to the bud tip using actin
filaments [98–100]. Myo4, unlike other type V myosins, is
a nonprocessive monomer in vivo, but it becomes processive
when present in the form of oligomers [101, 102].
Purification of the localization complex associated with a
single localization element revealed that multiple copies of
Myo4 are associated with this RNA [103]. Moreover,
increasing the number of Myo4 attached to the ASH1
mRNA increased the efficiency of localization of this
transcript. These results suggest that each localization
element interacts with higher order protein complexes in
which a She2 tetramer may recruit multiple copies of
Myo4, thus ensuring a continuous and processive movement
of the mRNP complex into the bud. Moreover, it is
possible that a She2 tetramer binds simultaneously to the
localization elements of a single transcript or, alternatively,
to those of different mRNAs. This would bring multiple
mRNAs together within a single complex in which several
Myo4 molecules modulate their transport to the bud tip
[103].
Even if the localization of a transcript occurs independently
of a molecular motor, redundant elements may still
be required for efficient localization. An example is the
Drosophila nanos mRNA, which is localized by a diffusion-based
mechanism at the posterior pole during late
stages of oogenesis, allowing abdominal and germ cell
development (see ‘‘mRNA diffusion and entrapment’’
540 K. Shahbabian, P. Chartrand
123
Fig. 2a–e Schematic presentation of different mechanisms of mRNA
localization. a Diffusion and entrapment of Xcat2 mRNA in the
mitochondrial cloud during early oogenesis in Xenopus. The movement
of the mitochondrial cloud toward the vegetal cortex during
stages 2–4 (indicated by a thick arrow) leads to the localization of this
mRNA at the vegetal pole. b Selective stabilization of Hsp83 mRNA
at the posterior pole of Drosophila embryo. Smaug protein triggers
the degradation of unlocalized Hsp83 transcripts elsewhere in the
embryo. c Localization of the ASH1 mRNA to the bud tip of yeast
cells. Upon transcription and nuclear export, this mRNA is actively
transported by a myosin-based mechanism on actin filaments.
d Localization of oskar and bicoid mRNA in Drosophila oocytes.
During Drosophila oogenesis, oskar and bicoid mRNA are synthesized
in the nurse cells, transported into the ooplasm, and localize to
the posterior and anterior poles of the oocyte, respectively. Arrows
indicate the movement and direction of RNP complexes along the
microtubules. e In immature neurons, b-actin mRNA is actively
transported to the neuronal growth cone through microtubule-based
transport
Control of cytoplasmic mRNA localization 541
123
section above) [26–29]. Nanos mRNA contains cis-acting
elements in its 30
UTR that are sufficient for posterior
localization [104]. These localization elements are located
in a large and complex region of 547 nucleotides, which
consists of partially redundant sequence elements, named
?1 to ?4. The combination of these four localization
elements is necessary for complete localization of nanos
mRNA [105]. However, a 41 nt region within element ?20
,
called the minimal element (ME), which is highly conserved
between D. melanogaster and D. virilis, was shown
to be sufficient for localization when present in three copies
[106]. So far, two trans-acting factors have been found
to interact with the nanos mRNA localization elements.
Rumpelstiltskin (Rump), a Drosophila homolog of hnRNP
M, which was previously described as a protein of 75 kD
(p75), interacts directly and specifically with the 50
region
of the ?20
element in vitro and in vivo [106, 107].
Mutations that disrupt the binding of Rump abolish the
localization capacity of the ?20
element, suggesting a role
for this protein in the localization of nanos mRNA. However,
the fact that some mutations disrupt localization but
not Rump binding suggests that other factors are also
needed for proper nanos mRNA localization. Indeed,
recent evidence suggest that Aubergine, a protein previously
shown to be required for oskar mRNA localization
and translational control, is also involved in nanos mRNA
localization. However Aubergine’s effect on nanos seems
to be independent of its role in RNA silencing (see above)
and oskar mRNA localization [108, 109].
Different localization elements act together to promote
mRNA localization
The presence of several localization elements in the same
transcript can be a way to recruit different trans-acting
factors, each one having a specific role in the localization
process or both having redundant functions. In chicken
embryo fibroblasts (CEFs), the b-actin mRNA localizes at
the lamellipodia, which results in fibroblast’s polarity and
motility [110]. Localization of this transcript depends on
active transport on the actin cytoskeleton and is directed by
a 54 nt zipcode element that is situated in the 30
UTR of the
mRNA, immediately downstream of the stop codon [111].
In the absence of the 54 nt element, another element of
43 nt was found to have a suboptimal activity for the
localization process. The two localization elements share
two submotifs, GGACU and AAUGC, which are both
necessary for the localization. However, a high A/C content
region in the 54 nt zipcode, which is absent in the
43 nt element, was suggested to confer a maximum
localization activity to the transcript [111]. The 54 nt zipcode
serves as a binding site for the Zipcode binding
protein 1 (ZBP1) [112]. Both the GGACU and A/C rich
motifs of this zipcode play an important role in this interaction,
as revealed by in vitro selection and mutagenesis
[111, 113]. In contrast, the distal 43 nt zipcode does not
interact with ZBP1, suggesting that other trans-acting
factors may interact with the 43 nt element and mediate
mRNA localization.
In the central nervous system, the Myelin basic protein
(MBP) mRNA is localized at the myelin compartment of
oligodendrocytes, a process essential for myelin biogenesis
[114]. Transport and localization of MBP mRNA is
directed by two distinct regions located in the 30
UTR of the
transcript. One is an element called the RNA transport
signal (RTS), which mediates MBP mRNA transport along
oligodendrocytes to the myelin sheath [115]. The RTS
element is composed of 21 nucleotides and serves as the
binding site for the heterogeneous nuclear ribonucleoprotein
(hnRNP) A2 [116]. In addition, localization and
anchoring of MBP mRNA to the myelin compartment is
mediated by another region called the RNA localization
region (RLR). This region of 340 nucleotides forms stable
secondary structures that are conserved across rat, mouse,
and human MBP mRNA. Interestingly, the RLR is only
necessary for localization of mRNA containing coding
sequences. In reporter RNA constructs in which the coding
region is deleted, RTS can direct both transport and
localization of the transcript, suggesting that different
pathways are involved in the localization of coding and
non-coding mRNA constructs [115].
The Vg1 mRNA is another good example of the role of
different and redundant localization elements in mediating
mRNA localization. The Vg1 maternal mRNA, which
encodes a member of the TGF-b family, is localized to the
vegetal cortex of Xenopus embryos during mid-oogenesis
[117, 118]. This transcript requires a 340 nucleotide
localization element in its 30
UTR to promote localization to
the vegetal pole of embryos [78]. Characterization of this
localization element revealed the presence of four repeated
sequence elements, termed E1 to E4, present in two to five
copies in the 30
UTR, and another element, termed VM1,
present in three copies [76, 119]. Element E2 was found to
interact with the RNA-binding protein Vera/Vg1 RBP,
which is involved in Vg1 mRNA localization [76, 79].
Deletion of elements E1, E4, and particularly E2, decreases
the interaction with Vera and either impairs or abolishes
Vg1 mRNA localization. The element VM1 was found to
recruit the RNA-binding protein PTB/hnRNP I, which
is involved in remodeling the interaction between Vg1
mRNA and Vera/Vg1 RBP [119, 120]. Interestingly,
duplication of the VM1 element is sufficient to promote the
localization of a reporter mRNA to the vegetal pole of
Xenopus laevis embryos [119]. However, clusters of five
VM1 elements or E2 elements from the 30
UTR of the
Xenopus borealis Vg1 mRNA are insufficient to promote
542 K. Shahbabian, P. Chartrand
123
mRNA localization separately, suggesting that clusters of
E2 and VM1 elements are both necessary for vegetal
localization [121].
Different localization elements act at various steps
of the localization pathway
The presence of different localization elements within a
transcript may be necessary to determine different steps of
a pathway leading to the final localization of the mRNA. In
this case, each localization element would specify a particular
step in the localization process, and each step would
be coupled to the preceding one. The combination of all
these elements together would result in a specific localization
pathway. For instance, during early stages of
oogenesis in Xenopus, the Xcat-2 mRNA localizes at the
vegetal cortex of oocytes via a diffusion and entrapment
mechanism (see above) [31]. As mentioned above, Xcat-2
mRNA first accumulates within a region of the MC called
the METRO and subsequently localizes at the vegetal
cortex [33, 34]. Xcat-2 mRNA localization requires two
distinct cis-acting elements: a 250 nt localization signal
called Mitochondrial Cloud Localization Element (MCLE),
which is located at the 50
end of the 30
UTR and is
responsible for the entrapment of Xcat-2 in the MC [122],
and a 164 nt germinal granule localization element
(GGLE), situated immediately downstream of MCLE,
which further directs the localization of Xcat-2 to the
germinal granules within the MC [123]. Interestingly,
fusion of the Xcat-2 GGLE motif to the mitochondrial
cloud localized mRNA Xlsirt resulted in the accumulation
of the Xlsirt chimera in germinal granules, suggesting that
the combination of both MC localization element and the
GGLE is required for localization at the germinal granules
[123].
In Drosophila, several transcripts contain multiple subdomains
in their 30
UTR that act as a localization element at
different stages of development. For example, during
oogenesis, oskar is synthesized in nurse cells and subsequently
transferred and localized at the posterior pole of
adjacent oocytes in the egg chamber (Fig. 2d) [124].
Proper localization of oskar mRNA is essential for posterior
body patterning and germ cell determination.
Different cis-acting elements within the 30
UTR of this
transcript are implicated in different steps of this process:
(1) movement of the transcript from the nurse cells to the
oocyte, (2) transient accumulation at the anterior pole, and
finally (3) posterior pole localization [125]. Mutations in a
region of the oskar 30
UTR that disrupts early localization
steps affect subsequent steps, suggesting that localization
of oskar mRNA takes place in distinct stages, and early
localization events are needed for later events to proceed
normally [125].
The bicoid mRNA is transcribed in the nurse cells
during stages 4 and 5 of oogenesis, transported into the
oocyte, and becomes localized to the anterior pole of the
oocyte during late oogenesis [126]. This transport requires
an intact microtubule network and dynein [127]. The bicoid
transcript contains several cis-acting elements residing in
its 30
UTR that are required for both transfer from nurse
cells to the oocyte and its proper anterior localization.
A region of 625 nt that is capable of forming secondary
structures consisting of multiple stem-loops is necessary
and sufficient for this localization [128, 129]. By using
several transgenes containing a small deletion in the
30
UTR, an element of 50 nt named BLE1 (bicoid localization
element 1) was found to be essential for the early
steps of the localization process [130]. This localization
element is composed of a stem-loop structure in which the
specific nucleotide sequence is not important for activity,
but rather it is the secondary structure that plays a crucial
role. Adjacent to the stem-loop are nucleotides whose
identities are important for proper localization [131].
Several other secondary structures in the 30
UTR of this
transcript direct localization of the bicoid mRNA in later
steps of localization. For instance, a stem-loop in Domain
V of bicoid 30
UTR interacts with Vps36, a member of the
ESCRT-II complex (endosomal sorting complex required
for transport), which is composed of three subunits: Vps22,
Vps25, and Vps36 [132]. This interaction is important for
bicoid mRNA localization, as mutants of ESCRT-II display
impaired localization of this transcript to the anterior pole
in late stages. Interestingly, dimerization of bicoid mRNA
is proposed to be important for these later localization
events. This phenomenon is directed by a stem-loop situated
in Domain III of the 30
UTR which is suggested to form
a recognition site for trans-acting factors such as Staufen
[133]. Interaction of Staufen with the extensive stem-loop
structure situated in the 30
UTR of bicoid leads to formation
of an mRNP complex that localizes at the anterior pole in a
microtubule-dependent manner [134]. A recent study
reported that Staufen and dynein are present in the same
particle as bicoid mRNA at the anterior pole, supporting a
role of Staufen in the localization of this transcript [135].
While Staufen and ESCRT-II are involved in bicoid
mRNA localization in late phases of development (S11 and
onward), the protein Exuperantia is required during earlier
phases, for transport from nurse cells to anterior pole
localization following transfer into the oocyte [136].
The gurken mRNA is a transcript localized at the posterior
pole of Drosophila oocytes during early stages of
oogenesis (stages 1–6), and to the dorsal anterior corner
during later stages (stages 8–9) [137, 138]. The localization
elements of this transcript are found in both 50
and 30
untranslated regions, as well as in some parts of the coding
sequence [24, 139]. These multiple elements are needed for
Control of cytoplasmic mRNA localization 543
123
the two-step localization pattern of this mRNA at the different
stages of oogenesis. The 50
UTR contains signals that
direct mRNA localization in the early stages, while a
region in the 50
coding sequence promotes accumulation
and/or stabilization of the transcript in the anterior cortical
ring during mid-oogenesis [24]. Further analysis of the
coding sequence showed that a short region of 64 nt that is
capable of forming a stem-loop is sufficient for apical
localization [140]. Interestingly, this element is also found
in the I factor RNA, a non-LTR retrotransposon that shows
the same two-step localization pattern as gurken mRNA
[140]. The 30
UTR of gurken mRNA also contains cis-acting
elements that are necessary to restrict this transcript to
the dorsal anterior corner during later stages of oogenesis
[24].
Control of molecular motors by localization elements
Besides their role in defining the final destination of an
mRNA, localization elements can also modulate the
activity or identity of molecular motors associated with a
transcript. Evidence for this mechanism came from live
cell imaging of the Drosophila hairy mRNA, one of the
pair-rule transcripts such as fushi tarazu (ftz), runt, and
wingless that localize apically of the peripheral nuclei in
the Drosophila syncytial stage embryos [141]. Hairy
mRNA localization depends on the following: two partially
redundant stem-loop structures, SL1 and SL2a, present in
its 30
UTR [142]; the proteins Egalitarian (Egl) and Bic-D
[143, 144]; and the minus-end molecular motor dynein
[145]. Microinjection of fluorescently labeled RNA in the
Drosophila blastoderm revealed that hairy mRNA, like
non-localizing transcripts, displays bidirectional transport,
suggesting that motors with opposite polarity associate
with this transcript [146]. However, unlike non-localized
transcripts, hairy mRNA spends more time undergoing
minus-end transport toward the apical pole. Interestingly,
increasing the number of localization elements in hairy
mRNA doubles the speed of apical trafficking compared to
wild-type mRNA, suggesting that these elements increase
the number of minus-end motors recruited to the transcript
[146]. Recently, work by Bullock and colleagues [147]
revealed that these stem-loops are bound by the RNAbinding
protein Egalitarian (Egl), which interacts with the
dynein cofactor Bic-D to recruit the molecular motor
dynein. Since Egl also binds to dynein light-chain (Dlc), a
regulator of dynein’s motor activity, this suggests a model
in which Egl can recruit an mRNA to dynein via Bic-D and
stimulate the activity of this motor via Dlc [147].
An additional mechanism through which a zipcode can
modulate mRNA localization is by the ability to recruit
different molecular motors. For instance, localization of the
b-actin mRNA to the leading edge of fibroblasts depends
on the actin cytoskeleton, suggesting a myosin-based
transport, while the localization of the same transcript at
the growth cone of neurons is microtubule dependent,
pointing instead toward kinesin-based transport [148, 149].
Since both localization events depend on the ZBP1 protein,
this suggests that this factor can recruit different motors
according to the cellular context. Another example was
observed in Xenopus oocytes, in which localization of the
Vg1 mRNA to the vegetal pole depends on both kinesin-1
and kinesin-2. While kinesin-1 interacts with the Vg1
localization element (VLE), kinesin-1 also interacts with
kinesin-2, and both motors carry out overlapping functions
in RNA transport [150].
Extracellular signaling and control of mRNA
localization
Another mechanism by which cells can control the cytoplasmic
localization of specific mRNA is via signal
transduction pathways, especially through extracellular
signaling. The first evidence that signal transduction
pathways control mRNA localization came from the study
of b-actin mRNA localization in fibroblast [151, 152].
Indeed, while b-actin mRNA normally localizes at the
leading edge of chicken fibroblasts, it displays a diffuse
cytoplasmic distribution in serum-starved fibroblasts.
Interestingly, addition of serum results in a rapid relocalization
of this transcript to the leading edge of the cells.
Addition of growth factors, such as PDGF or lysophosphatidic
acid (LPA), has the same effect of promoting
b-actin mRNA localization [151, 152], suggesting that
growth signaling pathways induce b-actin mRNA localization
at the leading edge. However, these growth factors
are also known to promote the polymerization of the actin
cytoskeleton via the small GTPases Rac and Rho [153].
Therefore, it is not clear if these signaling pathways
act directly on the mRNA localization machinery or indirectly
by promoting stress fiber formation or via both
mechanisms.
Most evidence supporting a role of signaling pathways
in promoting mRNA localization comes from studies in
neurons, in which several transcripts are localized to dendrites
or in the axon [21, 154]. The adult neuron is
constituted of dendritic trees that contain over 10,000
dendritic spines, each corresponding to a single excitatory
synapse. In these synapses, hundreds of different proteins
are known to be present. Long-term potentiation (LTP) or
long-term depression (LTD), two phenomena at the base of
memory, are induced by high frequency stimulation or
low frequency stimulation (respectively) of excitatory
synapses. These stimulations result in the activation of
specific receptors at the synapses, such as the metabotropic
544 K. Shahbabian, P. Chartrand
123
glutamate (mGluR) or N-methyl D-aspartate (NMDAR)
receptors, which trigger downstream signaling cascades
[155]. Maintenance of LTP or LTD depends on gene
expression and local translation of transcripts localized at
the excited synapses [21]. Therefore, synaptic activation in
neurons is an excellent system to study the role of signaling
pathways in promoting the transport and localization of
mRNAs.
Seminal studies on the Arc/Arg3.1 mRNA provided the
first evidence that synaptic activity can promote the
localization of a specific mRNA in dendrites. Arc is among
the immediate-early genes activated following seizures,
learning experiences, or induction of LTP (reviewed in
[156]). Using high frequency activation of perforant path
synapses in vivo, Steward and colleagues [157] observed
that newly transcribed Arc mRNA localizes at the activated
synapses, suggesting that extracellular signaling promotes
both transcription and transport of this transcript. Interestingly,
when Arc mRNA is induced in the absence of a
localized synaptic signal (in the case of a generalized seizure
for instance), this mRNA was uniformly distributed in
dendrites. Only the subsequent activation of synapses led to
the transport and localization of Arc mRNA to the activated
synapses [157]. This selective targeting of Arc mRNA
was shown to depend on the activation of the N-methyl
D-aspartate receptor (NMDAR) [158], suggesting that a
specific signaling pathway can control the transport and
localization of mRNA to synapses. Besides Arc, several
other transcripts, including BDNF and TrkB [159], CamKIIa
[160], b-actin [161], and AMPA receptor subunits
GluR1 and GluR2 [162], were also found to localize in
dendrites of cultured neurons following synapse activation.
Other studies revealed that not only synaptic activity but
also nerve growth factors stimulate mRNA localization in
neurons. Axon outgrowth responds to attractive signals,
i.e., neurotrophic factors, in order to guide the axonal
growth cone and establish wiring between neurons [163].
Among the intracellular responses to these signals, local
translation of mRNA localized at the growth cone participates
in the movement and directional steering of the axon
[164]. For instance, neurotrophin-3 (NT-3) was initially
found to induce localization of the b-actin mRNA to the
growth cones of forebrain neurons [149, 165]. Other
growth factors, such as the brain derived neurotrophic
factor (BDNF) or Netrin-1, also induce b-actin mRNA
localization to the growth cones of X. laevis neurons
[166, 167] and in rat cortical neurons [168].
Axonal localization of specific mRNAs can also be
controlled by growth factors, such as the myo-inositol
monophosphate 1 (Impa1) mRNA, which is induced to
localize to distal axons by nerve growth factor (NGF) [12].
Interestingly, mRNA profiling in axons revealed that neurotrophins
can specifically increase or decrease the levels
of individual mRNAs in the axon [11]. For instance, neurotrophins
that favor axon growth (e.g., NGF, BDNF, and
NT-3) regulate the axonal level of a number of mRNAs.
However, factors that act as inhibitors of axon growth (e.g.,
myelin-associated glycoprotein and semaphorin 3A) regulate
a distinct set of axonal mRNAs and induce an opposite
effect on the transcripts regulated by NGF, BDNF, and
NT-3 [11]. Importantly, these effects occurred on preexisting
pools of mRNA, since an inhibitor of RNA polymerase
II was included during the treatments with growth
factors. These results suggest that the regulation of mRNA
localization is very specific at the level of individual
mRNAs and for the different extracellular cues that activate
similar signaling pathways.
Controlling the motility and directionality
of RNA granules
A question raised by these results is how a signaling
pathway can control the localization of a specific mRNA.
Live-cell imaging of neuronal cells provided some insights
into possible mechanisms behind the effect of signaling
pathways on mRNA transport and localization. Initial livecell
imaging studies using the nucleic acid dye SYTO 14
revealed the presence of mobile RNA granules in the
dendrites of cultured neurons [169]. Upon addition of
neurotrophin-3, the number and motility of these RNA
granules rapidly increased within 5–15 min post-stimulation
[170]. By coexpression of a reporter mRNA containing
the 30
UTR of the CamKIIa mRNA and MS2 stem-loops
with the green fluorescent protein fused to the MS2 RNAbinding
protein, Rook and colleagues [171] were able to
visualize GFP-tagged CamKII 30
UTR RNA granules in the
dendrites of cultured neurons. In the absence of neuronal
activation, RNA granules exhibited either oscillatory,
anterograde (away from the cell body), or retrograde
(toward the cell body) movements. Interestingly, neuronal
depolarization using KCl resulted in a shift toward anterograde
movement of the RNA granules within dendrites.
Similar effects were observed using a GFP-tagged ZBP1,
which binds the b-actin mRNA zipcode and promotes
localization of this transcript to the growth cones of neurons
[165]. GFP-ZBP1 forms granules that contain b-actin
mRNA and display bidirectional movements in neurites
[165]. However, 15 min after KCl exposure of neurons, the
level of GFP-ZBP1 particles in dendrites was significantly
increased, suggesting a rapid localization of a pre-existing
somatic pool of ZBP1 molecules instead of de novo synthesis
of GFP-ZBP1 [161].
Altogether, these results suggest that localized transcripts
are packed into granules containing both
microtubule plus-end and minus-end molecular motors,
i.e., kinesin and dynein. Biochemical studies support these
Control of cytoplasmic mRNA localization 545
123
results, as large RNA granules (over 1,000S) from mouse
brain were purified by affinity chromatography using the
C-terminal cargo-binding domain of the kinesin-1 Kif5 as
bait [172]. These granules were found to contain the
mRNA CamKIIa and Arc, and RNA-binding proteins
associated with mRNA transport (Pura, staufen, FMRP),
protein synthesis, and RNA metabolism. Another approach
to purify RNA transport granules from developing rat brain
by biochemical fractionations revealed the presence of the
kinesin Kif5, dynein, ZBP1, and b-actin mRNA in these
granules, but not the CamKIIa mRNA [173]. Both results
suggest that RNA granules are heterogeneous and that their
content can vary depending on the stage of development.
Nevertheless, the presence of both kinesin and dynein in
the same granule could result in a ‘‘tug-of-war’’ between
both molecular motors, leading to the oscillatory or bidirectional
movement observed for the RNA granules by
live-cell imaging [171]. This is supported by the observation
of similar bidirectional transport of RNA granules
containing GFP-labeled Kif5 [172], ZBP1 [165], or Staufen
[174].
The observation that synaptic activity promotes anterograde
movement of RNA granules suggests that, upon
activation of a signaling pathway, subsequent phosphorylation
of a specific factor in the RNA granules may favor
anterograde over retrograde transport. Evidence for such a
‘‘molecular switch’’ mechanism has been obtained for
vesicular transport in neurons [175]. In these vesicles, the
huntingtin protein acts as a scaffold that recruits both
dynein and kinesin. Huntingtin binds directly to the dynein
motor, but indirectly with the p150Glued
subunit of dynactin
and kinesin-1 via the huntingtin-associated protein-1
(HAP1) [176, 177]. In its unphosphorylated form, kinesin-1
interacts weakly with the motor complex associated with
huntingtin, and vesicles are prone to retrograde transport.
Upon phosphorylation of huntingtin at Ser421 by the kinase
Akt, the interaction between kinesin-1 and the dynactin
motor complex increases, favoring anterograde transport.
Since huntingtin has been recently found to be associated
with dendritic RNA granules and is involved in their
transport [178], it is possible that huntingtin may play a
similar role in dendritic mRNA localization (Fig. 3a).
Modulation of the interaction between molecular
motors and RNA-binding proteins
Posttranslational modifications induced by the activated
signaling pathway can also modulate the association
between a molecular motor and the RNA-binding protein
that recruits the localized mRNA. Evidence for such a
mechanism comes from studies on the RNA-binding
Fragile X mental retardation protein (FMRP), which participates
both in dendritic mRNA transport and translational
repression of localized mRNA [179]. FMRP is involved in
the transport of the MAP1B and CamKIIa mRNAs into
dendrites following stimulation of the glutamate receptor
mGluR5 [180–182]. A recent study by Dictenberg and
colleagues [183] revealed that FMRP is associated with
Kif5 via the kinesin light chain (KLC) in neurons. Interestingly,
upon stimulation of glutamate receptor, the
amount of FMRP associated with Kif5 increases, while the
total amount of FMRP does not change, suggesting that
activation of the glutamate signaling pathway stimulates the
association between FMRP and the kinesin complex
(Fig. 3b). However, the molecular mechanism behind this
process is still unknown.
Local reorganization of the cytoskeleton
Finally, another mechanism by which signaling pathways
can control mRNA localization is by promoting a local
reorganization of the cytoskeleton. Evidence for this
mechanism comes from the work of Steward and colleagues
[184], who reported that polymerization of actin at
activated synapses is important for local Arc mRNA targeting.
The authors observed that inhibition of actin
polymerization by a Rho kinase inhibitor, or latrunculin B,
blocks Arc mRNA targeting to the activated synapse
but does not block Arc mRNA transport into dendrites.
Interestingly, both Arc mRNA localization and actin
polymerization at activated synapses depend on NMDA
receptor activity, suggesting that the signaling pathway
activated by this receptor coordinates both processes.
Finally, the authors also found that, besides actin polymerization,
activation of the Erk kinase via the MAP
kinase pathway is required for Arc mRNA localization.
These results suggest that following the long distance,
microtubule-based transport of Arc mRNA into dendrites,
the local polymerization of actin at an activated synapse is
required to either anchor Arc mRNA at this synapse or
transfer this mRNA to an actin-based motor for terminal
localization at spines inside the synapse (Fig. 3c) [184].
This last step may require the actin-dependent molecular
motor Myosin-Va, which has been reported to transport
mRNA/protein complexes in dendritic spines [185]. Surprisingly,
the Arc protein is required to stabilize F-actin at
active synapses [186], suggesting a positive feedback
between Arc protein localization and actin polymerization
at the synapse.
Conclusions
In this review, we have followed the travels of localized
mRNAs from their transcription in the nucleus, the
recruitment of localization factors to their zipcodes, their
546 K. Shahbabian, P. Chartrand
123
encounter with protein motors that can speed them on their
way, the extracellular signaling cascades that may change
their fate, and the arrival of these transcripts at their final
destination. We have reviewed in detail various mechanisms
by which trans-acting RNA-binding proteins and
cis-acting RNA sequences control localized transcripts in
different organisms and cell types. Although we have
underlined the importance of cis-acting localization elements
in this process, few of them have been well
characterized and we still know little about their interactions
with RNA-binding proteins. Furthermore, most of the
information on the control of mRNA localization comes
from in-depth studies on a select group of transcripts. The
advent of genome-wide studies, which lead to the identification
of numerous examples of localized mRNAs to
various cytoplasmic locations or organelles, opens the
possibility that some of these transcripts may use novel
mechanisms of localization and that control of their
localization may occur in different ways than the currently
studied localized mRNAs. This will require the identification
of localization elements in these transcripts and the
trans-acting binding factors that recognize these elements.
Moreover, for most of these mRNAs, the biological function
of their localization is still unclear. Finally, the
development of new methods to study mRNA localization
in real time has greatly increased our knowledge in this
Fig. 3a–c Signal transduction and mRNA localization. a Model of
huntingtin phosphorylation upon neuron stimulation. In the nonphosphorylated
state, huntingtin associates with dynein and more weakly
with kinesin, which results in either bidirectional or retrograde
transport of cargoes associated with huntingtin. In its phosphorylated
state, huntingtin binds more strongly to kinesin via HAP1 and
dynactin, which leads to anterograde transport of its cargoes,
including dendritic mRNAs. MTs Microtubules. b In dendrites,
FMRP-associated mRNAs are transported by kinesin upon mGluR
activation. mGluR stimulation increases the interaction between
kinesin light chain (KLC) and FMRP. KHC Kinesin heavy chain.
c Arc/Arg3.1 mRNA localization to synapses following NMDA
receptor (NMDAR) stimulation. Upon NMDAR stimulation (1), the
Erk and Rho kinases are activated (2), promoting actin polymerization
in the synapse (3). mRNA granules in a translational-inactive state are
transported in dendrites along the microtubules by kinesin. Actin
polymerization leads to the transfer of RNA granules into the synapse,
via the myosin V molecular motor (4), which transports its cargo into
activated synapses (5)
Control of cytoplasmic mRNA localization 547
123
field [187]. However, most of these studies have been
performed in cultured cells or embryo, and little is known
about mRNA localization in a whole animal during its
development or pathogenesis. The recent development of
transgenic mice for in vivo detection of an endogenous
mRNA at high resolution opens the possibility of dealing
with such questions [188]. These are only some of the new
challenges that await the field for the future.
Acknowledgments We thank Emmanuelle Querido and E´ric
Le´cuyer for critical reading of the manuscript, and Kim Mowry, Gary
Bassell, and E´ric Le´cuyer for providing images. This work was
supported by the Grant MOP43855 from the Canadian Institutes for
Health Research (CIHR). P.C is a Senior Scholar from the Fond de
Recherche en Sante´ du Que´bec (FRSQ).
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