Intracellular mRNA localization: motors move messages

UAP56 RNA helicase is required for axis specification and cytoplasmic mRNA localization in Drosophila

mRNA export from the nucleus requires the RNA helicase UAP56 and involves remodeling of ribonucleo-protein complexes in the nucleus. Here, we show that UAP56 is required for bulk mRNA export from the nurse cell nuclei that supply most of the material to the growing Drosophila oocyte and for the organization of chromatin in the oocyte nucleus. Loss of UAP56 function leads to patterning defects that identify uap56 as a spindle-class gene similar to the RNA helicase Vasa. UAP56 is required for the localization of gurken, bicoid and oskar mRNA as well as post-translational modification of Osk protein. By injecting grk RNA into the oocyte cytoplasm, we show that UAP56 plays a role in cytoplasmic mRNA localization. We propose that UAP56 has two independent functions in the remodeling of ribonucleo-protein complexes. The first is in the nucleus for mRNA export of most transcripts from the nucleus. The second is in the cytoplasm for remodeling the transacting factors that decorate mRNA and dictate its cytoplasmic destination.

Dynein regulates epithelial polarity and the apical localization of stardust A mRNA

Intense investigation has identified an elaborate protein network controlling epithelial polarity. Although precise subcellular targeting of apical and basolateral determinants is required for epithelial architecture, little is known about how the individual determinant proteins become localized within the cell. Through a genetic screen for epithelial defects in the Drosophila follicle cells, we have found that the cytoplasmic Dynein motor is an essential regulator of apico–basal polarity. Our data suggest that Dynein acts through the cytoplasmic scaffolding protein Stardust (Sdt) to localize the transmembrane protein Crumbs, in part through the apical targeting of specific sdt mRNA isoforms. We have mapped the sdt mRNA localization signal to an alternatively spliced coding exon. Intriguingly, the presence or absence of this exon corresponds to a developmental switch in sdt mRNA localization in which apical transcripts are only found during early stages of epithelial development, while unlocalized transcripts predominate in mature epithelia. This work represents the first demonstration that Dynein is required for epithelial polarity and suggests that mRNA localization may have a functional role in the regulation of apico–basal organization. Moreover, we introduce a unique mechanism in which alternative splicing of a coding exon is used to control mRNA localization during development.

Cells within epithelial sheets are highly polarized with distinct apical and basolateral membrane domains. This cellular organization is critical to both epithelial form and function, and a failure to maintain epithelial polarity is often linked to tumor progression. The protein network that establishes and maintains the two membrane domains relies on the precise subcellular localization of its molecular components, but little is known about how these proteins are targeted to their sites of action. We have shown that the localization of the apical determinant protein Stardust depends on the microtubule motor Dynein. While investigating the relationship between Dynein and Stardust, we also made two unexpected observations about stardust mRNA regulation. First, the mechanism by which Dynein localizes Stardust may depend, in part, on the apical targeting of the stardust mRNA. Second, some stardust mRNA is apically localized during early stages of epithelial development, but the selective removal of the apical localization signal leads to the sole production of uniformly localized transcripts in mature epithelial cells. Together, these results introduce roles for Dynein in apico–basal polarity regulation and raise important questions about the role of mRNA localization in the targeting of polarity determinant proteins and epithelial maturation.

Morphogenesis in giant-celled algae

The giant-celled algae, which consist of cells reaching millimeters in size, some even centimeters, exhibit unique cell architecture and physiological characteristics. Their cells display a variety of morphogenetic phenomena, that is, growth, division, differentiation, and reproductive cell formation, as well as wound-healing responses. Studies using immunofluorescence microscopy and pharmacological approaches have shown that microtubules and/or actin filaments are involved in many of these events through the generation of intracellular movement of cell components or entire protoplasmic contents and the spatial control of cell activities in specific areas of the giant cells. A number of environmental factors including physical stimuli, such as light and gravity, invoke localized but also generalized cellular reactions. These have been extensively investigated to understand the regulation of morphogenesis, in particular addressing cytoskeletal and endomembrane dynamics, electrophysiological elements affecting ion fluxes, and the synthesis and mechanical properties of the cell wall. Some of the regulatory pathways involve signal transduction and hormonal control, as in other organisms. The giant unicellular green alga Acetabularia, which has proven its usefulness as an experimental model in early amputation/grafting experiments, will potentially once again serve as a useful model organism for studying the role of gene expression in orchestrating cellular morphogenesis.

Nuclear RNA export factor 7 is localized in processing bodies and neuronal RNA granules through interactions with shuttling hnRNPs

The nuclear RNA export factor (NXF) family proteins have been implicated in various aspects of post-transcriptional gene expression. This study shows that mouse NXF7 exhibits heterologous localization, i.e. NXF7 associates with translating ribosomes, stress granules (SGs) and processing bodies (P-bodies), the latter two of which are believed to be cytoplasmic sites of storage, degradation and/or sorting of mRNAs. By yeast two-hybrid screening, a series of heterogeneous nuclear ribonucleoproteins (hnRNPs) were identified as possible binding partners for NXF7. Among them, hnRNP A3, which is believed to be involved in translational control and/or cytoplasmic localization of certain mRNAs, formed a stable complex with NXF7 in vitro. Although hnRNP A3 was not associated with translating ribosomes, it was co-localized with NXF7 in P-bodies. After exposing to oxidative stress, NXF7 trans-localized to SGs, whereas hnRNP A3 did not. In differentiated neuroblastoma Neuro2a cells, NXF7 was co-localized with hnRNP A3 in cell body and neurites. The amino terminal half of NXF7, which was required for stable complex formation with hnRNP A3, coincided with the region required for localization in both P-bodies and neuronal RNA granules. These findings suggest that NXF7 plays a role in sorting, transport and/or storage of mRNAs through interactions with hnRNP A3.

Cholesterol level regulates endosome motility via Rab proteins

The role of cholesterol in the regulation of endosome motility was investigated by monitoring the intracellular trafficking of endocytosed folate receptors (FRs) labeled with fluorescent folate conjugates. Real-time fluorescence imaging of HeLa cells transfected with green fluorescent protein-tubulin revealed that FR-containing endosomes migrate along microtubules. Moreover, microinjection with antibodies that inhibit microtubule-associated motor proteins demonstrated that dynein and kinesin I participate in the delivery of FR-containing endosomes to the perinuclear area and plasma membrane, respectively. Further, single-particle tracking analysis revealed bidirectional motions of FR endosomes, mediated by dynein and kinesin motors associated with the same endosome. These experimental tools allowed us to use FR-containing endosomes to evaluate the impact of cholesterol on intracellular membrane trafficking. Lowering plasma membrane cholesterol by metabolic depletion or methyl-beta-cyclodextrin extraction was found to both increase FR-containing endosome motility and change endosome distribution from colocalization with Rab7 to colocalization with Rab4. These data provide evidence that cholesterol regulates intracellular membrane trafficking via modulation of the distribution of low molecular weight G-proteins that are adaptors for microtubule motors.

The Saccharomyces cerevisiae Pus2 protein encoded by YGL063w ORF is a mitochondrial tRNA:Psi27/28-synthase

The RNA:pseudouridine (Psi)-synthase family is one of the most complex families of RNA modification enzymes. Ten genes encoding putative RNA:Psi-synthases have been identified in S. cerevisiae. Most of the encoded enzymes have been characterized experimentally. Only the putative RNA:Psi-synthase Pus2p (encoded by the YGL063w ORF) had no identified substrate. Here, we analyzed Psi residues in cytoplasmic and mitochondrial tRNAs extracted from S. cerevisiae strains, carrying disruptions in the PUS1 and/or PUS2 ORFs. Our results demonstrate that Pus2p is a mitochondrial-specific tRNA:Psi-synthase acting at positions 27 and 28 in tRNAs. The importance of the Asp56 residue in the conserved ARTD motif of the Pus2p catalytic site is demonstrated in vivo. Interestingly, in spite of the absence of a characteristic N-terminal targeting signal, our data strongly suggest an efficient and rapid targeting of Pus2p in yeast mitochondria. In contradiction with the commonly held idea that a unique nuclear gene encodes the enzyme required for both cytoplasmic and mitochondrial tRNA modifications, here we show the existence of an enzyme specifically dedicated to mitochondrial tRNA modification (Pus2p), the corresponding modification in cytoplasmic tRNAs being catalyzed by another protein (Pus1p).

Drosophila Squid/hnRNP helps Dynein switch from a gurken mRNA transport motor to an ultrastructural static anchor in sponge bodies

In Drosophila oocytes, dorso-anterior transport of gurken mRNA requires both the Dynein motor and the heterogeneous nuclear ribonucleoprotein (hnRNP) Squid. We show that gurken transcripts are transported directly on microtubules by Dynein in nonmembranous electron-dense transport particles that also contain Squid and the transport cofactors Egalitarian and Bicaudal-D. At its destination, gurken mRNA is statically anchored by Dynein within large electron-dense cytoplasmic structures known as sponge bodies. Egalitarian and Bicaudal-D contribute only to active transport, whereas Dynein and Squid are also required for gurken mRNA anchoring and the integrity of sponge bodies. Disrupting Dynein function disperses gurken mRNA homogeneously throughout the cytoplasm, whereas the loss of Squid function converts the sponge bodies into active transport particles. We propose that Dynein acts as a static structural component for the assembly of gurken mRNA transport and anchoring complexes, and that Squid is required for the dynamic conversion of transport particles to sponge bodies.

Drosophila Dynein light chain (DDLC1) binds to gurken mRNA and is required for its localization

During oogenesis in Drosophila, mRNAs encoding determinants required for the polarization of egg and embryo become localized in the oocyte in a spatially restricted manner. The TGF-alpha like signaling molecule Gurken has a central role in the polarization of both body axes and the corresponding mRNA displays a unique localization pattern, accumulating initially at the posterior and later at the anterior-dorsal of the oocyte. Correct localization of gurken RNA requires a number of cis-acting sequence elements, a complex of trans-acting proteins, of which only several have been identified, and the motor proteins Dynein and Kinesin, traveling along polarized microtubules. Here we report that the cytoplasmic Dynein-light-chain (DDLC1) which is the cargo-binding subunit of the Dynein motor protein, directly bound with high specificity and affinity to a 230-nucleotide region within the 3'UTR of gurken, making it the first Drosophila mRNA-cargo to directly bind to the DLC. Although DDLC1 lacks known RNA-binding motifs, comparison to double-stranded RNA-binding proteins suggested structural resemblance. Phenotypic analysis of ddlc1 mutants supports a role for DDLC1 in gurken RNA localization and anchoring as well as in correct positioning of the oocyte nucleus.

NXF2 is involved in cytoplasmic mRNA dynamics through interactions with motor proteins

Tap/NXF1, the founding member of the evolutionarily conserved NXF (Nuclear RNA export Factor) family of proteins, is required for the nuclear export of bulk poly(A)+ RNAs. In mice, three additional NXF family genes (NXF2, NXF3, NXF7) have been identified and characterized to date. Cumulative data suggest that NXF family members play roles, not only in nuclear mRNA export, but also in various aspects of post-transcriptional mRNA metabolism. In order to better understand the functional role of NXF2, we searched for its binding partners by yeast two-hybrid screening and identified several cytoplasmic motor proteins, including KIF17. The interaction of NXF2 with KIF17, which was confirmed by GST pull-down and co-immunoprecipitation assays, is mediated by the N-terminal domain of NXF2, which is required for the punctate localization patterns in dendrites of primary neurons. We also found that the NXF2-containing dendritic granules, which were co-localized with KIF17, mRNA and Staufen1, a known component of neuronal mRNA granules, moved bidirectionally along dendrites in a microtubule-dependent manner. These results suggest that NXF2, a nucleo-cytoplasmic mRNA transporter, plays additional roles in the cytoplasmic localization of mRNAs through interactions with cytoplasmic motor proteins.

RNA localization signals: deciphering the message with bioinformatics

mRNA localization is an important posttranscriptional method of targeting proteins to their site of function. The sorting of transcripts to their correct intracellular destination is achieved by a number of mechanisms, including selective degradation or transport by molecular motors along the cytoskeleton. In all cases, this involves mRNA localization signals, or so called zip codes, being recognized by trans-acting cellular factors. In a few cases, primary sequence motifs for RNA localization can be identified, but in general, localization signals operate at the level of secondary (2D) and tertiary (3D) structure. This inevitably means that searching for localization signal motifs is a complex task requiring specialist knowledge of bioinformatics. Furthermore, the publications describing these searching methods tend to be aimed at the bioinformatics community. In this review, we have surveyed the major tools for folding, comparing, and searching potential mRNA localization signals in transcripts or across genomes. Our aim is to provide an overview for biologists, who lack specialist computer and bioinformatics training, of the major RNA bioinformatics tools that are available. The examples provided are focused on mRNA localization signals and RNA stem-loop structures, however, these tools can be applied to the study of any RNA signals.

Dynamics of bidirectional transport of Arc mRNA in neuronal dendrites

The mRNA for Arc (activity-regulated cytoskeletal protein) is delivered into dendrites and localizes selectively at active synapses. Here we use a green fluorescent protein-based labeling system and confocal microscopy to define the transport kinetics of exogenously expressed mRNA from chimaeric Arc constructs (Arc/MS2 mRNA) in the dendrites of living rat neurons in culture. Arc/MS2 mRNA assembles into particles that move independently, bidirectionally, and intermittently in a fashion indicative of transport. Transport velocities range from below 6 to 65 mum/minute, which is consistent with actin-based and microtubule-based transport, respectively. In general, orthograde translocations are longer than retrograde translocations. Rapidly translocating Arc/MS2 mRNA particles sometimes reverse direction and decrease velocity just before stopping, suggesting that local signals regulate Arc mRNA targeting movements. These observations identify several phases of Arc mRNA movement that serve as potential points for regulating Arc mRNA localization.

The genetics of axonal transport and axonal transport disorders

Neurons are specialized cells with a complex architecture that includes elaborate dendritic branches and a long, narrow axon that extends from the cell body to the synaptic terminal. The organized transport of essential biological materials throughout the neuron is required to support its growth, function, and viability. In this review, we focus on insights that have emerged from the genetic analysis of long-distance axonal transport between the cell body and the synaptic terminal. We also discuss recent genetic evidence that supports the hypothesis that disruptions in axonal transport may cause or dramatically contribute to neurodegenerative diseases.

Pathways for mRNA localization in the cytoplasm

Studies of the intracellular localization of mRNA have clearly demonstrated that certain subsets of mRNA are concentrated in discrete locations within the cytoplasm. Localization is one aspect of the post-transcriptional control of gene expression, and is intertwined with the translation and turnover of mRNA to achieve the goal of local protein production. Different mechanisms have been identified that enable localized mRNAs to target different subcellular compartments, and recent advances in understanding these pathways is reviewed here.

A genetic screen in Drosophila for genes interacting with senseless during neuronal development identifies the importin moleskin

Senseless (Sens) is a conserved transcription factor required for normal development of the Drosophila peripheral nervous system. In the Drosophila retina, sens is necessary and sufficient for differentiation of R8 photoreceptors and interommatidial bristles (IOBs). When Sens is expressed in undifferentiated cells posterior to the morphogenetic furrow, ectopic IOBs are formed. This phenotype was used to identify new members of the sens pathway in a dominant modifier screen. Seven suppressor and three enhancer complementation groups were isolated. Three groups from the screen are the known genes Delta, lilliputian, and moleskin/DIM-7 (msk), while the remaining seven groups represent novel genes with previously undefined functions in neural development. The nuclear import gene msk was identified as a potent suppressor of the ectopic interommatidial bristle phenotype. In addition, msk mutant adult eyes are extremely disrupted with defects in multiple cell types. Reminiscent of the sens mutant phenotype, msk eyes demonstrate reductions in the number of R8 photoreceptors due to an R8 to R2,5 fate switch, providing genetic evidence that Msk is a component of the sens pathway. Interestingly, in msk tissue, the loss of R8 fate occurs earlier than with sens and suggests a previously unidentified stage of R8 development between atonal and sens.

Self-assembly driven by molecular motors

The outcome of a self-assembly process is not only determined by the specified connections between building blocks, but also by the means of bringing building blocks into contact and of testing for the formation of an intended connection. Endowing each building block with the ability to actively move overcomes some limitations of diffusion-driven molecular and nanoscale self-assembly by accelerating transport, reducing unwanted connections, and introducing self-organization phenomena with desirable consequences. Proof-of-principle experiments utilizing biomolecular motors, motor proteins, to propel nanostructures and the underlying concepts are reviewed, and the potential impact for nanomanufacturing is discussed.

mRNA localization to the mitochondrial surface allows the efficient translocation inside the organelle of a nuclear recoded ATP6 protein

As previously established in yeast, two sequences within mRNAs are responsible for their specific localization to the mitochondrial surface-the region coding for the mitochondrial targeting sequence and the 3'UTR. This phenomenon is conserved in human cells. Therefore, we decided to use mRNA localization as a tool to address to mitochondria, a protein that is not normally imported. For this purpose, we associated a nuclear recoded ATP6 gene with the mitochondrial targeting sequence and the 3'UTR of the nuclear SOD2 gene, which mRNA exclusively localizes to the mitochondrial surface in HeLa cells. The ATP6 gene is naturally located into the organelle and encodes a highly hydrophobic protein of the respiratory chain complex V. In this study, we demonstrated that hybrid ATP6 mRNAs, as the endogenous SOD2 mRNA, localize to the mitochondrial surface in human cells. Remarkably, fusion proteins localize to mitochondria in vivo. Indeed, ATP6 precursors synthesized in the cytoplasm were imported into mitochondria in a highly efficient way, especially when both the MTS and the 3'UTR of the SOD2 gene were associated with the re-engineered ATP6 gene. Hence, these data indicate that mRNA targeting to the mitochondrial surface represents an attractive strategy for allowing the mitochondrial import of proteins originally encoded by the mitochondrial genome without any amino acid change in the protein that could interfere with its biologic activity.

Miranda couples oskar mRNA/Staufen complexes to the bicoid mRNA localization pathway

The double-stranded RNA binding protein Staufen is required for the microtubule-dependent localization of bicoid and oskar mRNAs to opposite poles of the Drosophila oocyte and also mediates the actin-dependent localization of prospero mRNA during the asymmetric neuroblast divisions. The posterior localization of oskar mRNA requires Staufen RNA binding domain 2, whereas prospero mRNA localization mediated the binding of Miranda to RNA binding domain 5, suggesting that different Staufen domains couple mRNAs to distinct localization pathways. Here, we show that the expression of Miranda during mid-oogenesis targets Staufen/oskar mRNA complexes to the anterior of the oocyte, resulting in bicaudal embryos that develop an abdomen and pole cells instead of the head and thorax. Anterior Miranda localization requires microtubules, rather than actin, and depends on the function of Exuperantia and Swallow, indicating that Miranda links Staufen/oskar mRNA complexes to the bicoid mRNA localization pathway. Since Miranda is expressed in late oocytes and bicoid mRNA localization requires the Miranda-binding domain of Staufen, Miranda may play a redundant role in the final step of bicoid mRNA localization. Our results demonstrate that different Staufen-interacting proteins couple Staufen/mRNA complexes to distinct localization pathways and reveal that Miranda mediates both actin- and microtubule-dependent mRNA localization.

Assembling an intermediate filament network by dynamic cotranslation

We have been able to observe the dynamic interactions between a specific messenger RNA (mRNA) and its protein product in vivo by studying the synthesis and assembly of peripherin intermediate filaments (IFs). The results show that peripherin mRNA-containing particles (messenger ribonucleoproteins [mRNPs]) move mainly along microtubules (MT). These mRNPs are translationally silent, initiating translation when they cease moving. Many peripherin mRNPs contain multiple mRNAs, possibly amplifying the total amount of protein synthesized within these "translation factories." This mRNA clustering is dependent on MT, regulatory sequences within the RNA and the nascent protein. Peripherin is cotranslationally assembled into insoluble, nonfilamentous particles that are precursors to the long IF that form extensive cytoskeletal networks. The results show that the motility and targeting of peripherin mRNPs, their translational control, and the assembly of an IF cytoskeletal system are linked together in a process we have termed dynamic cotranslation.

Characterization of an RNA granule from developing brain

In brain, mRNAs are transported from the cell body to the processes, allowing for local protein translation at sites distant from the nucleus. Using subcellular fractionation, we isolated a fraction from rat embryonic day 18 brains enriched for structures that resemble amorphous collections of ribosomes. This fraction was enriched for the mRNA encoding beta-actin, an mRNA that is transported in dendrites and axons of developing neurons. Abundant protein components of this fraction, determined by tandem mass spectrometry, include ribosomal proteins, RNA-binding proteins, microtubule-associated proteins (including the motor protein dynein), and several proteins described only as potential open reading frames. The conjunction of RNA-binding proteins, transported mRNA, ribosomal machinery, and transporting motor proteins defines these structures as RNA granules. Expression of a subset of the identified proteins in cultured hippocampal neurons confirmed that proteins identified in the proteomics were present in neurites associated with ribosomes and mRNAs. Moreover many of the expressed proteins co-localized together. Time lapse video microscopy indicated that complexes containing one of these proteins, the DEAD box 3 helicase, migrated in dendrites of hippocampal neurons at the same speed as that reported for RNA granules. Although the speed of the granules was unchanged by activity or the neurotrophin brain-derived neurotrophic factor, brain-derived neurotrophic factor, but not activity, increased the proportion of moving granules. These studies define the isolation and composition of RNA granules expressed in developing brain.

Poly(A)+ RNA and cytoskeleton during cyst formation in the cap ray of Acetabularia peniculus

The configuration and distribution of polyadenylated RNA (poly(A)+ RNA) during cyst formation in the cap rays of Acetabularia peniculus were demonstrated by fluorescence in situ hybridization using oligo(dT) as a probe, and the spatial and functional relationships between poly(A)+ RNA and microtubules or actin filaments were examined by immunofluorescence microscopy and cytoskeletal inhibitor treatment. Poly(A)+ RNA striations were present in the cytoplasm of early cap rays and associated with longitudinal actin bundles. Cytochalasin D destroyed the actin filaments and caused a dispersal of the striations. Poly(A)+ RNA striations occurred in the cytoplasm of the cap rays up to the stage when secondary nuclei migrated into the cap rays, but they disappeared after the secondary nuclei were settled in their positions. At that time, a mass of poly(A)+ RNA was present around each of the secondary nuclei and accumulated rRNA. This mass colocalized with microtubules radiating from the surface of each secondary nucleus and disappeared when the microtubules were depolymerized by butamifos, which did not affect the configuration of actin filaments. These masses of poly(A)+ RNA continued to exist even after the cap ray cytoplasm divided into cyst domains. Thus two distinct forms of poly(A)+ RNA population, striations and masses, appear in turn at consecutive stages of cyst formation and are associated with distinct cytoskeletal elements, actin filaments and microtubules, respectively.

Centriolar Mechanisms of Differentiation and Replicative Aging of Higher Animal Cells

The centrosome (centriole) and the cytoskeleton produced by it are structures, which probably determine differentiation, morphogenesis, and switching on the mechanism of replicative aging in all somatic cells of multicellular animals. The mechanism of such programming of the events seems to include cytoskeleton influences and small RNAs related to the centrosome. 1) If these functions are really related with centrioles, the multicellular organism's cells which: a) initially lack centrioles (e.g., higher plant cells and also zygote and early blastomeres of some animals) or cytoskeleton (e.g., embryonic stem cells); or b) generate centrioles de novo (e.g., zygote and early blastomeres of some animals), will be totipotent and lack replicative aging. Consequently, the absence (constant or temporary) of the structure determining the counting of divisions also means the absence of counting of differentiation processes. 2) Although a particular damage to centrioles or cytoskeleton (e.g., in tumor cells) fails to make the cells totipotent (because the morphogenetic status of these cells, as differentiated from that of totipotent ones, is not zero), but such a transformation can suppress the initiation of the aging mechanism induced by these structures and, thus, make such cells replicatively "immortal".

The role of the cytoskeleton during viral infection

Upon infection, virions or subviral nucleoprotein complexes are transported from the cell surface to the site of viral transcription and replication. During viral egress, particles containing viral proteins and nucleic acids again move from the site of their synthesis to that of virus assembly and further to the plasma membrane. Because free diffusion of molecules larger than 500 kDa is restricted in the cytoplasm, viruses as well as cellular organelles employ active, energy-consuming enzymes for directed transport. This is particularly evident in the case of neurotropic viruses that travel long distances in the axon during retrograde or anterograde transport. Viruses use two strategies for intracellular transport: Viral components either hijack the cytoplasmic membrane traffic or they interact directly with the cytoskeletal transport machinery. In this review we describe how viruses--particularly members of the Herpesviridae, Adenoviridae, Parvoviridae, Poxviridae, and Baculoviridae--make use of the microtubule and the actin cytoskeleton. Analysing the underlying principles of viral cytosolic transport will be helpful in the design of viral vectors to be used in research as well as human gene therapy, and in the identification of new antiviral target molecules.

An eleven nucleotide section of the 3'-untranslated region is required for perinuclear localization of rat metallothionein-1 mRNA

Localization of mRNAs provides a novel mechanism for synthesis of proteins close to their site of function. MT1 (metallothionein-1) is a small, metal-binding protein that is largely cytoplasmic but which can be found in the nucleus. The localization of rat MT1 requires the perinuclear localization of its mRNA by a mechanism dependent on the 3'-UTR (3'-untranslated region). The present study investigates the nature of this mRNA localization signal using Chinese-hamster ovary cells transfected with gene constructs in which either MT1 or the globin coding region is linked to different sequences from the MT1 3'-UTR. Deletion, mutagenesis and antisense oligonucleotide approaches indicate that nt 45-76 of the 3'-UTR, in particular nt 66-76, are required for the localization of either MT1 mRNA or chimaeric transcripts in which a beta-globin coding region is linked to sequences from the MT1 3'-UTR. This section of the 3'-UTR contains a CACC repeat. Two mutations that are predicted to alter the secondary structure of this region also impair localization. Our hypothesis is that the perinuclear localization signal in MT1 mRNA is formed by a combination of the CACC repeat and its structural context.

gurken and the I factor retrotransposon RNAs share common localization signals and machinery

Drosophila gurken mRNA is localized by dynein-mediated transport to a crescent near the oocyte nucleus, thus targeting the TGFalpha signal and forming the primary embryonic axes. Here, we show that gurken and the I factor, a non-LTR retrotransposon, share a small consensus RNA stem loop of defined secondary structure, which forms a conserved signal for dynein-mediated RNA transport to the oocyte nucleus. Furthermore, gurken and the I factor compete in vivo for the same localization machinery. I factor transposition leads to its mRNA accumulating near and within the oocyte nucleus, thus causing perturbations in gurken and bicoid mRNA localization and axis specification. These observations further our understanding of the close association of transposable elements with their host and provide an explanation for how I factor transposition causes female sterility. We propose that the transposition of other elements may exploit the host's RNA transport signals and machinery.

Dynein anchors its mRNA cargo after apical transport in the Drosophila blastoderm embryo

Molecular motors actively transport many types of cargo along the cytoskeleton in a wide range of organisms. One class of cargo is localized mRNAs, which are transported by myosin on actin filaments or by kinesin and dynein on microtubules. How the cargo is kept at its final intracellular destination and whether the motors are recycled after completion of transport are poorly understood. Here, we use a new RNA anchoring assay in living Drosophila blastoderm embryos to show that apical anchoring of mRNA after completion of dynein transport does not depend on actin or on continuous active transport by the motor. Instead, apical anchoring of RNA requires microtubules and involves dynein as a static anchor that remains with the cargo at its final destination. We propose a general principle that could also apply to other dynein cargo and to some other molecular motors, whereby cargo transport and anchoring reside in the same molecule.

RNA-binding proteins in early development

RNA-binding proteins play a major part in the control of gene expression during early development. At this stage, the majority of regulation occurs at the levels of translation and RNA localization. These processes are, in general, mediated by RNA-binding proteins interacting with specific sequence motifs in the 3'-untranslated regions of their target RNAs. Although initial work concentrated on the analysis of these sequences and their trans-acting factors, we are now beginning to gain an understanding of the mechanisms by which some of these proteins function. In this review, we will describe a number of different families of RNA-binding proteins, grouping them together on the basis of common regulatory strategies, and emphasizing the recurrent themes that occur, both across different species and as a response to different biological problems.

Nuclear localization signal peptides induce molecular delivery along microtubules

Many essential processes in eukaryotic cells depend on regulated molecular exchange between its two major compartments, the cytoplasm and the nucleus. In general, nuclear import of macromolecular complexes is dependent on specific peptide signals and their recognition by receptors that mediate translocation through the nuclear pores. Here we address the question of how protein products bearing such nuclear localization signals arrive at the nuclear membrane before import, i.e., by simple diffusion or perhaps with assistance of cytoskeletal elements or cytoskeleton-associated motor proteins. Using direct single-particle tracking and detailed statistical analysis, we show that the presence of nuclear localization signals invokes active transport along microtubules in a cell-free Xenopus egg extract. Chemical and antibody inhibition of minus-end directed cytoplasmic dynein blocks this active movement. In the intact cell, where microtubules project radially from the centrosome, such an interaction would effectively deliver nuclear-targeted cargo to the nuclear envelope in preparation for import.

A Rae1-containing ribonucleoprotein complex is required for mitotic spindle assembly

Centrosome-independent microtubule polymerization around chromosomes has been shown to require a local gradient of RanGTP, which discharges mitotic cargoes from the nuclear import receptor importin beta. Here, we have used an activity-based assay in Xenopus egg extracts to purify the mRNA export protein Rae1 as a spindle assembly factor regulated by this pathway. Rae1 is a microtubule-associated protein that binds directly to importin beta. Depletion of Rae1 from extracts or cells severely inhibits mitotic spindle assembly. A purified Rae1 complex stabilizes microtubules in egg extracts in a RanGTP/importin beta-regulated manner. Interestingly, Rae1 exists in a large ribonucleoprotein complex, which requires RNA for its activity to control microtubule dynamics in vitro. Furthermore, we provide evidence that RNA associates with the mitotic spindle and that it plays a direct, translation-independent role in spindle assembly. Our studies reveal an unexpected function for RNA in spindle morphogenesis.

Subcellular localization and trafficking of polycystins

Polycystin-2 is a member of the transient receptor potential (TRP) family of ion channels that is mutated in autosomal dominant polycystic kidney disease. Although its function as a non-selective cation channel has been demonstrated in several model systems, the precise subcellular localization of polycystin-2 (TRPP2) in tubular epithelial cells has remained controversial. Recent evidence suggests that the subcellular localization of TRPP2 is regulated by multiple protein interactions. This review will summarize our current knowledge about polycystin trafficking and highlight the experimental data that supports a compartment-specific function of 'cystogenic' proteins.

tRNA-linked molecular beacons for imaging mRNAs in the cytoplasm of living cells

When oligonucleotide probes are microinjected into cells to image the distribution of RNAs, they are rapidly sequestered into the nucleus. As a result, it is difficult to detect mRNAs in the cytoplasm of living cells. We were able to overcome this process by attaching tRNA transcripts to the probes. We show that when fluorescently labeled tRNAs, tRNAs with extensions at their 5′ end, or chimeric molecules in which a molecular beacon possessing a 2′-O-methylribonucleotide backbone is linked to a tRNA, are injected into the nucleus of HeLa cells, they are exported into the cytoplasm. When these constructs are introduced into the cytoplasm, they remain cytoplasmic. These constructs allow the distribution of both the general mRNA population and specific mRNAs to be imaged in living cells. This strategy should also be useful for enhancing the efficacy of antisense oligonucleotides by keeping them in the cytoplasm. Our observations show that the fidelity of the tRNA export system is relaxed for unnatural tRNA variants when they are introduced into the nucleus in large amounts.

Polarised distribution of the RNA-binding protein Staufen in differentiated intestinal epithelial cells

mRNA localisation, as a mechanism for directing localised protein synthesis, plays a vital role in the functioning of certain cells, such as neurons and oocytes. Potentially this mechanism may also occur in polarised intestinal epithelial cells. Here we show that Staufen1(55), a protein involved in mRNA localisation and transport, is asymmetrically distributed in differentiated Caco-2 intestinal epithelial cells and partly co-localised with calnexin, a marker of the endoplasmic reticulum. The localisation to the apical region of the cell indicates that Staufen may be involved in localisation of transcripts to this domain.

Annexin A2 binds to the localization signal in the 3' untranslated region of c-myc mRNA

Messenger RNA trafficking, which provides a mechanism for local protein synthesis, is dependent on cis-acting sequences in the 3' untranslated regions (3'UTRs) of the mRNAs concerned acting together with trans-acting proteins. The C-MYC transcription factor is a proto-oncogene product involved in cell proliferation, differentiation and apoptosis. Localization of c-myc mRNA to the perinuclear cytoplasm and its association with the cytoskeleton is determined by a signal in the 3'UTR. Here we show the specific binding of a trans-acting factor to the perinuclear localization element in the 3'UTR of c-myc mRNA and identify this protein as annexin A2. Gel retardation and UV cross-linking experiments showed that proteins in fibroblast extracts formed complexes with the region of c-myc 3'UTR implicated in localization; a protein of approximately 36 kDa exhibited specific, Ca(2+)-dependent binding. Binding was reduced by introduction of a mutation that abrogates localization. Using RNA-affinity columns followed by gel electrophoresis and mass spectrometry this protein was identified as annexin A2. The RNA-protein complex formed by cell extracts was further retarded by anti-(annexin A2). Purified annexin A2 bound to the same region of the c-myc 3'UTR but binding was reduced by introduction of a mutation, as with cell extracts. It is proposed that binding of annexin A2 to the localization signal in the c-myc mRNA leads to association with the cytoskeleton and perinuclear localization. The data indicate a novel functional role for the RNA-binding properties of annexin A2 in perinuclear localization of mRNA and the association with the cytoskeleton.

PLAUF is a novel P. lividus sea urchin RNA-binding protein

Preliminary results have shown that various proteins bind long 3'UTR of the transcript for Paracentrotus lividus sea urchin H3.3 histone variant and are probably implicated in mRNA instability. In order to identify these RNA-binding proteins, we screened a lambda-ZAPII cDNA expression library prepared from poly(A) mRNA extracted from sea urchin embryos at blastula stage. We isolated a cDNA that codes for a novel RNA-binding protein homologous to rat and human AUF1 family proteins and we refer to it as PLAUF. Proteins present in the whole lysate of the phages expressing PLAUF bound specifically in vitro the 3'UTR of the H3.3 histone transcript. Northern blot analysis revealed three PLAUF transcripts that are already present in unfertilized eggs; during development their amount increased starting from 4-blastomere embryos and reached the plateau at blastula stage. While the transcription start point was unique, longer 3'UTRs were revealed by 3'RACE approach and further cDNA library screening. Moreover RT-PCR showed the presence of at least one alternative spliced mRNA that codes for a protein with different COOH terminus. The structure of the PLAUF gene was determined by screening a P. lividus sea urchin genomic library with the PLAUF cDNA as probe. Analysis of the positive clones showed that the PLAUF gene is split in 10 exons and 9 introns spanning a distance of about 10 kb. Moreover we demonstrated that the exon 9 was alternative spliced during mRNA processing.

Exercise-induced gene expression changes in the rat spinal cord

There is growing evidence that exercise benefits recovery of neuromuscular function from spinal cord injury (SCI). However, the effect of exercise on gene expression in the spinal cord is poorly understood. We used oligonucleotide microarrays to compare thoracic and lumbar regions of spinal cord of either exercising (voluntary wheel running for 21 days) or sedentary rats. The expression data were filtered using statistical tests for significance, and K-means clustering was then used to segregate lists of significantly changed genes into sets based upon expression patterns across all experimental groups. Levels of brain-derived neurotrophic factor (BDNF) protein were also measured after voluntary exercise, across different regions of the spinal cord. BDNF mRNA increased with voluntary exercise, as has been previously shown for other forms of exercise, contributed to by increases in both exon I and exon III. The exercise-induced gene expression changes identified by microarray analysis are consistent with increases in pathways promoting neuronal health, signaling, remodeling, cellular transport, and development of oligodendrocytes. Taken together these data suggest cellular pathways through which exercise may promote recovery in the SCI population.

N-terminal kinesins: many and various

Molecular motors are a fascinating group of proteins that have vital roles in a huge variety of cellular processes. They all share the ability to produce force through the hydrolysis of adenosine triphosphate, and fall into classes groups: the kinesins, myosins and the dyneins. The kinesin superfamily itself can be split into three major groups depending on the position of the motor domain, which is localized N-terminally, C-terminally, or internally. This review focuses on the N-terminal kinesins, providing a brief overview of their roles within the cell, and illustrating recent key developments in our understanding of how these proteins function.

Transport of Drosophila fragile X mental retardation protein-containing ribonucleoprotein granules by kinesin-1 and cytoplasmic dynein

Transport and translation of mRNA are tightly coupled to ensure strict temporal and spatial expression of nascent proteins. Fragile X mental retardation protein (FMRP) has been shown to be involved in translational regulation and is found in ribonucleoprotein (RNP) granules that travel along dendrites of neurons. In this study, GFP-tagged Drosophila homologue of FMRP (dFMR) was used to visualize RNP granule movement in Drosophila S2 cells. GFP-dFMR form granules that contain both endogenous dFMR and mRNA. Live fluorescence microscopy revealed that dFMR-containing RNP granules move bidirectionally in thin processes formed by S2 cells in the presence of cytochalasin D. Knocking down the heavy chains of either kinesin-1 (kinesin heavy chain) or cytoplasmic dynein (dynein heavy chain) by RNA interference blocks the movement of the dFMR granules. In contrast, knockdown of kinesin light chain (KLC), which is typically necessary for movement of membrane organelles by kinesin-1, had no effect on the dFMR granule translocation. In immunoprecipitation assays, dFMR associates with both kinesin heavy chain and dynein heavy chain, but not KLC. Based on these findings, we conclude that dFMR-containing RNP granules are moved by both kinesin-1 and cytoplasmic dynein and that KLC is not essential and is likely missing from RNP-transporting kinesin-1.

A systems view of mRNP biology

Gene expression occurs through a complex mRNA-protein (mRNP) system that stretches from transcription to translation. Gene expression processes are increasingly studied from global perspectives in order to understand their pathways, properties, and behaviors as a system. Here we review these beginnings of mRNP systems biology, as they have emerged from recent large-scale investigation of mRNP components, interactions, and dynamics. Such work has begun to lay the foundation for a broader, integrated view of mRNP organization in gene expression.

Myocyte differentiation generates nuclear invaginations traversed by myofibrils associating with sarcomeric protein mRNAs

Certain types of cell both in vivo and in vitro contain invaginated or convoluted nuclei. However, the mechanisms and functional significance of the deformation of the nuclear shape remain enigmatic. Recent studies have suggested that three types of cytoskeleton, microfilaments, microtubules and intermediate filaments, are involved in the formation of nuclear invaginations, depending upon cell type or conditions. Here, we show that undifferentiated mouse C2C12 skeletal muscle myoblasts had smoothsurfaced spherical or ellipsoidal nuclei, whereas prominent nuclear grooves and invaginations were formed in multinucleated myotubes during terminal differentiation. Conversion of mouse fibroblasts to myocytes by the transfection of MyoD also resulted in the formation of nuclear invaginations after differentiation. C2C12 cells prevented from differentiation did not have nuclear invaginations, but biochemically differentiated cells without cell fusion exhibited nuclear invaginations. Thus, biochemical differentiation is sufficient for the nuclear deformation. Although vimentin markedly decreased both in the biochemically and in the terminally differentiated cells, exogenous expression of vimentin in myotubes did not rescue nuclei from the deformation. On the other hand, non-striated premyofibrils consisting of sarcomeric actinmyosin filament bundles and cross-striated myofibrils traversed the grooves and invaginations. Time-lapse microscopy showed that the preformed myofibrillar structures cut horizontally into the nuclei. Prevention of myofibril formation retarded the generation of nuclear invaginations. These results indicate that the myofibrillar structures are, at least in part, responsible for the formation of nuclear grooves and invaginations in these myocytes. mRNA of sarcomeric proteins including myosin heavy chain and alpha-actin were frequently associated with the myofibrillar structures running along the nuclear grooves and invaginations. Consequently, the grooves and invaginations might function in efficient sarcomeric protein mRNA transport from the nucleus along the traversing myofibrillar structures for active myofibril formation.

She2p Is a Novel RNA Binding Protein with a Basic Helical Hairpin Motif

Selective transport of mRNAs in ribonucleoprotein particles (mRNP) ensures asymmetric distribution of information within and among eukaryotic cells. Actin-dependent transport of ASH1 mRNA in yeast represents one of the best-characterized examples of mRNP translocation. Formation of the ASH1 mRNP requires recognition of zip code elements by the RNA binding protein She2p. We determined the X-ray structure of She2p at 1.95 A resolution. She2p is a member of a previously unknown class of nucleic acid binding proteins, composed of a single globular domain with a five alpha helix bundle that forms a symmetric homodimer. After demonstrating potent, dimer-dependent RNA binding in vitro, we mapped the RNA binding surface of She2p to a basic helical hairpin in vitro and in vivo and present a mechanism for mRNA-dependent initiation of ASH1 mRNP complex assembly.

mRNA localization and the cytoskeleton

mRNA localization is a widespread post-transcriptional mechanism for targeting protein synthesis to specific cellular sites. It is involved in the generation of cell polarity, asymmetric segregation of cell fate determinants and germ cell specification. Actin and microtubule filaments have key functions during RNA localization, especially during transport of mRNAs and anchoring at target sites. Recent advances in understanding the role of motors and filament systems have mainly resulted from the contribution of live imaging of mRNA movement and from the purification of putative localization ribonucleoproteins. There have also been new findings on the role of centrosomes in RNA localization.

Nuclear bodies and compartments: functional roles and cellular signalling in health and disease

There is much interest in recent years in the possible role of different nuclear compartments and subnuclear domains in the regulation of gene expression, signalling, and cellular functions. The nucleus contains inositol phosphates, actin and actin-binding proteins and myosin isoforms, multiple protein kinases and phosphatases targeting Cdk-1 and Cdk-2, MAPK/SAPK, and Src-related kinases and their substrates, suggesting the implication of several signalling pathways in the intranuclear organization and function of nuclear bodies (NBs). NBs include the well-characterized Cajal bodies (CBs; or coiled bodies), the nucleolus, perinucleolar and perichromatin regions, additional NBs best illustrated by the promyelocytic leukemia nuclear bodies [PML-NBs, also named PML oncogenic dots (PODs), ND10, Kr-bodies] and similar intranuclear foci containing multi-molecular complexes with major role in DNA replication, surveillance, and repair, as well as messenger RNA and ribosomal RNA synthesis and assembly. Chromatin modifying proteins, such as the CBP acetyltransferase and type I histone deacetylase, accumulate at PML-NBs. PML-NBs and Cajal bodies are very dynamic and mobile within the nuclear space and are regulated by cellular stress (heat shock, apoptosis, senescence, heavy metal exposure, viral infection, and DNA damage responses). NBs strongly interact, using signalling mechanisms for the directional and ordered traffic of essential molecular components. NBs organize the delivery and storage of essential RNAs and proteins that play a role in transcription, pre-mRNA biosynthesis and splicing, and the sequestration and/or degradation of regulatory proteins, such as heterogenous nuclear ribonuclear proteins (hnRNPs), p53, Rb1, CBP, STAT3, and others. The objective of this review is to summarize some aspects of these nuclear structures/bodies/domains, including their proposed roles in cellular signalling and in human diseases, mainly neurodegenerative disorders and cancer.

Sequential dimerization of human zipcode-binding protein IMP1 on RNA: a cooperative mechanism providing RNP stability

Active cytoplasmic RNA localization depends on the attachment of RNA-binding proteins that dictate the destination of the RNA molecule. In this study, we used an electrophoretic mobility-shift assay in combination with equilibrium and kinetic analyses to characterize the assembly of the human zipcode-binding protein IMP1 on targets in the 3'-UTR from Igf-II mRNA and in H19 RNA. In both cases, two molecules of IMP1 bound to RNA by a sequential, cooperative mechanism, characterized by an initial fast step, followed by a slow second step. The first step created an obligatory assembly intermediate of low stability, whereas the second step was the discriminatory event that converted a putative RNA target into a 'locked' stable RNP. The ability to dimerize was also observed between members of the IMP family of zipcode-binding proteins, providing a multitude of further interaction possibilities within RNP granules and with the localization apparatus.

A late role for the association of hnRNP A2 with the HIV-1 hnRNP A2 response elements in genomic RNA, Gag, and Vpr localization

Two cis-acting RNA trafficking sequences (heterogenous ribonucleoprotein A2 (hnRNP A2)-response elements 1 and 2 or A2RE-1 and A2RE-2) have been identified in HIV-1 vpr and gag mRNAs and were found to confer cytoplasmic RNA trafficking in a murine oligodendrocyte assay. Their activities were assessed during HIV-1 proviral gene expression in COS7 cells. Single point mutations that were shown to severely block RNA trafficking were introduced into each of the A2REs. In both cases, this resulted in a marked decrease in hnRNP A2 binding to HIV-1 genomic RNA in whole cell extracts and hnRNP A2-containing polysomes. This also resulted in an accumulation of HIV-1 genomic RNA in the nucleus and a significant reduction in genomic RNA encapsidation levels. Immunofluorescence analyses revealed altered expression patterns for pr55Gag and particularly that for Vpr. Vpr localization became almost completely nuclear and this was reflected in a significant reduction in virion-associated Vpr levels. These effects coincided with late steps of the viral replication cycle and were not seen at early time points post-transfection. Transcription, splicing, steady state RNA levels, and pr55Gag processing were not affected. On the other hand, viral replication was markedly compromised in A2RE-2 mutant viruses and this correlated with lowered genomic RNA encapsidation levels. These data reveal new insights into the virus-host interactions between hnRNP A2 and the HIV-1 A2REs and their influence on the patterns of HIV-1 gene expression and viral assembly.

The ribosome receptor, p180, interacts with kinesin heavy chain, KIF5B

The conventional microtubule-dependent motor protein kinesin consists of heavy and light chains both of which have been documented to bind a variety of potential linker or cargo proteins. In this study we employed a yeast two-hybrid assay to identify additional binding partners of the kinesin heavy chain isoform KIF5B. A human brain cDNA library was screened with a bait corresponding to amino acid residues 814-963 of human KIF5B. This screen identified the ribosome receptor, p180, as a KIF5B-binding protein. The sites of interaction are residues 1294-1413 of p180 and the C-terminal half of the cargo binding-domain of KIF5B (residues 867-907). The KIF5B-binding site in p180 is homologous to the previously determined KIF5B-binding site in kinectin. The interacting regions of p180 and KIF5B consist almost entirely of heptad repeats, suggesting the interaction is a coiled-coil. A role for the kinesin/p180 interaction may include mRNA localization and/or transport of endoplasmic reticulum-derived vesicles.

The embryonic origins of left-right asymmetry

The bilaterally symmetric body plan of vertebrates features several consistent asymmetries in the placement, structure, and function of organs such as the heart, intestine, and brain. Deviations from the normal pattern result in situs inversus, isomerisms, or heterotaxia (independent randomization), which have significant clinical implications. The invariance of the left-right (LR) asymmetry of normal morphology, neuronal function, and phenotype of several syndromes raises fascinating and fundamental questions in cell, developmental, evolutionary, and neurobiology. While a pathway of asymmetrically expressed signaling factors has been well-characterized in several model systems, very early steps in the establishment of LR asymmetry remain poorly understood. In particular, the origin of consistently oriented asymmetry is unknown. Recently, a candidate for the origins of asymmetry has been suggested: bulk transport of extracellular morphogens by rotating primary cilia during gastrulation. This model is appealing because it 'bootstraps' morphological asymmetry of the embryo from the intrinsic structural (molecular) chirality of motile cilia. However, conceptual and practical problems remain with this hypothesis. Indeed, the genetic data are also consistent with a different mechanism: cytoplasmic transport roles of motor proteins. This review outlines the progress and remaining questions in the field of left-right asymmetry, and focuses on an alternative model for 'Step 1' of asymmetry. More specifically, based on wide-ranging data on ion fluxes and motor protein function in several species, it is suggested that laterality is driven by pH/voltage gradients across the midline, which are established by chiral movement of motor proteins with respect to the cytoskeleton.

Xenopus Staufen is a component of a ribonucleoprotein complex containing Vg1 RNA and kinesin

RNA localization is a key mechanism for generating cell and developmental polarity in a wide variety of organisms. We have performed studies to investigate a role for the Xenopus homolog of the double-stranded RNA-binding protein, Staufen, in RNA localization during oogenesis. We have found that Xenopus Staufen (XStau) is present in a ribonucleoprotein complex, and associates with both a kinesin motor protein and vegetally localized RNAs Vg1 and VegT. A functional role for XStau was revealed through expression of a dominant-negative version that blocks localization of Vg1 RNA in vivo. Our results suggest a central role for XStau in RNA localization in Xenopus oocytes, and provide evidence that Staufen is a conserved link between specific mRNAs and the RNA localization machinery.

mRNA localisation gets more complex

Recent advances in techniques for visualising mRNA movement in living cells have led to rapid progress in understanding the mechanism of mRNA localisation in the cytoplasm. There is an emerging consensus that in many cases the mRNA signals that determine intracellular destination are more complex and difficult to define than was first anticipated. Furthermore, the transacting factors that interpret the mRNA signals are numerous and their combinations change during the life of an mRNA, perhaps allowing the selection of many sub-destinations in the cell. Lastly, an emerging theme over the past few years is that many proteins that determine the destinations of mRNAs are recruited on nascent transcripts in the nucleus. They often function in many different processes in the biogenesis of mRNA and probably act in concert to provide specificity.

Dual FRET molecular beacons for mRNA detection in living cells

The ability to visualize in real-time the expression level and localization of specific endogenous RNAs in living cells can offer tremendous opportunities for biological and disease studies. Here we demonstrate such a capability using a pair of molecular beacons, one with a donor and the other with an acceptor fluorophore that hybridize to adjacent regions on the same mRNA target, resulting in fluorescence resonance energy transfer (FRET). Detection of the FRET signal significantly reduced false positives, leading to sensitive imaging of K-ras and survivin mRNAs in live HDF and MIAPaCa-2 cells. FRET detection gave a ratio of 2.25 of K-ras mRNA expression in stimulated and unstimulated HDF, comparable to the ratio of 1.95 using RT-PCR, and in contrast to the single-beacon result of 1.2. We further revealed intriguing details of K-ras and survivin mRNA localization in living cells. The dual FRET molecular beacons approach provides a novel technique for sensitive RNA detection and quantification in living cells.