RNA localization

Temporal and spatial control of gene expression in early embryos of farm animals

A gradual transition from oocyte-derived mRNA and proteins to full embryonic transcription characterises early embryonic development. Messenger RNAs and proteins of maternal origin are accumulated into the oocyte throughout its growth inthe ovary. Upon fertilisation, sev eral mechanisms ar e activated that controlthe appropriate use of such material and prepare for the synthesis of new products. The present review will describe some of the mechanisms active in early embryos of domestic species. Data will be presented on the control of gene expression by the 3' untranslated regions and their interaction with specialised sequences at the 5' cap end. The process of RNA sorting and localisation, initially described in different cell types and in oocytes of lower species, will also be discussed, particularly in relation to its possible role in regulating early pig development. Finally, specific genes involved in the activation of cattle embryonic transcription will be described. This brief overview will provide some suggestions on how these different mechanisms may be integrated and cooperate to ensure the correct initiation of embryonic development.

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.

The motility and dynamic properties of intermediate filaments and their constituent proteins

Intermediate filament (IF) proteins exist in multiple structural forms within cells including mature IF, short filaments or 'squiggles', and non-filamentous precursors called particles. These forms are interconvertible and their relative abundance is IF type, cell type- and cell cycle stage-dependent. These structures are often associated with molecular motors, such as kinesin and dynein, and are therefore capable of translocating through the cytoplasm along microtubules. The assembly of mature IF from their precursor particles is also coupled to translation. These dynamic properties of IF provide mechanisms for regulating their reorganization and assembly in response to the functional requirements of cells. The recent findings that IF and their precursors are frequently associated with signaling molecules have revealed new functions for IF beyond their more traditional roles as mechanical integrators of cells and tissues.

Direct observation of regulated ribonucleoprotein transport across the nurse cell/oocyte boundary

In Drosophila, the asymmetric localization of specific mRNAs to discrete regions within the developing oocyte determines the embryonic axes. The microtubule motors dynein and kinesin are required for the proper localization of the determinant ribonucleoprotein (RNP) complexes, but the mechanisms that account for RNP transport to and within the oocyte are not well understood. In this work, we focus on the transport of RNA complexes containing bicoid (bcd), an anterior determinant. We show in live egg chambers that, within the nurse cell compartment, dynein actively transports green fluorescent protein-tagged Exuperantia, a cofactor required for bcd RNP localization. Surprisingly, the loss of kinesin I activity elevates RNP motility in nurse cells, whereas disruption of dynein activity inhibits RNP transport. Once RNPs are transferred through the ring canal to the oocyte, they no longer display rapid, linear movements, but they are distributed by cytoplasmic streaming and gradually disassemble. By contrast, bcd mRNA injected into oocytes assembles de novo into RNP particles that exhibit rapid, dynein-dependent transport. We speculate that after delivery to the oocyte, RNP complexes may disassemble and be remodeled with appropriate accessory factors to ensure proper localization.

Cytoplasmic remodelling and the acquisition of developmental competence in pig oocytes

The progression of oocyte meiosis is accompanied by major changes in the ooplasm that play a key role in the completion of a coordinate nuclear and cytoplasmic maturation. We review evidence from the literature and present data obtained in our laboratory on different aspects of pig oocyte cytoplasm compartmentalization during maturation and early embryo development. In particular, we will discuss the changes in adenosine triphosphate (ATP) concentration and distribution taking place during the maturation process and their possible significance for oocyte developmental competence. We describe two important aspects of cytoplasmic streaming: mitochondrial distribution patterns in oocytes and early embryos and the complex rearrangements of cytoplasmic microtubule networks, while discussing their possible correlations with ooplasm compartmentalization. Recent evidence indicates that the cytoskeleton is used to shuttle not only organelles but also mRNAs to specific sites within the oocyte cytoplasm. Localization is driven by specific molecular motors belonging to the kinesin superfamily and requires the involvement of the RNA targeting molecule Staufen. We present recent experimental evidence, obtained in our laboratory, on the pig orthologues for kinesin KIF5B and Staufen, describe their expression patterns and discuss their possible role in oocyte maturation.

RNA localisation in the nervous system

The localisation of specific RNAs is a widely employed mechanism to generate asymmetry in various biological systems, e.g. during embryonic development and cellular differentiation. Here, we highlight the importance of RNA localisation in mature neurons. Specific examples of mRNAs localised in neurons are those encoding Arc, beta-actin, CaMKIIalpha and MAP2. Moreover, non-coding RNAs, such as BC1/BC200 and microRNAs (miRNAs), which play important roles in the translational regulation of localised mRNAs, receive increasing attention. The process of RNA localisation, including RNP biogenesis, transport, anchoring and translational control, and the importance of RNA localisation for the function of the nervous system are discussed.

Conserved features of germination and polarized cell growth: a few insights from a pollen-fern spore comparison

BACKGROUND

The germination of both pollen and fern spores results in the emergence of a cell-pollen tube from pollen, rhizoid from spore-that grows in a polar fashion, primarily at its apical end. In both of these tip-growing cells, the delivery of secretory vesicles to the growing end is guided in part by a calcium gradient, with calcium entering at the tip where it is most highly concentrated. The similarities between the two systems extend beyond tip-focused calcium gradients to encompass signalling pathways and elements including calmodulin, nitric oxide, annexins and Rop-GTPases.

SCOPE AND AIMS

This review is limited to those pathways and elements that function similarly in fern and pollen systems based on currently available evidence. The aim is to illustrate the common mechanisms by which tip growth occurs, facilitate further investigations into this area, and examine the implications for the evolutionarily conserved control of tip growth.

CONCLUSIONS

The interplay of calcium, nitric oxide and other effectors in both pollen and fern spores suggests certain signalling pathways became important regulators of germination and growth early in the evolution of land plants. Both large- and small-scale comparative genomic methods have shown to be promising in their ability to find new and relevant comparisons for further research. Cross-species comparisons may serve to speed up this process by highlighting both basic pathways and system-specific deviations.

Annexin A2 recognises a specific region in the 3'-UTR of its cognate messenger RNA

Annexin A2 is a multifunctional Ca(2+)- and lipid-binding protein. We previously showed that a distinct pool of cellular Annexin A2 associates with mRNP complexes or polysomes associated with the cytoskeleton. Here we report in vitro and in vivo experiments showing that Annexin A2 present in this subset of mRNP complexes interacts with its cognate mRNA and c-myc mRNA, but not with beta(2)-microglobulin mRNA translated on membrane-bound polysomes. The protein recognises sequence elements within the untranslated regions, but not within the coding region, of its cognate mRNA. Alignment of the Annexin A2-binding 3'-untranslated regions of annexin A2 mRNA from several species reveals a five nucleotide consensus sequence 5'-AA(C/G)(A/U)G. The Annexin A2-interacting region of the 3'-untranslated region can be mapped to a sequence of about 100 nucleotides containing two repeats of the consensus sequence. The binding elements appear to involve both single and double stranded regions, indicating that a specific higher order mRNA structure is required for binding to Annexin A2. We suggest that this type of interaction is representative for a group of mRNAs translated on cytoskeleton-bound polysomes.

Gene expression within a dynamic nuclear landscape

Molecular imaging in living cells or organisms now allows us to observe macromolecular assemblies with a time resolution sufficient to address cause-and-effect relationships on specific molecules. These emerging technologies have gained much interest from the scientific community since they have been able to reveal novel concepts in cell biology, thereby changing our vision of the cell. One main paradigm is that cells stochastically vary, thus implying that population analysis may be misleading. In fact, cells should be analyzed within time-resolved single-cell experiments rather than being compared to other cells within a population. Technological imaging developments as well as the stochastic events present in gene expression have been reviewed. Here, we discuss how the structural organization of the nucleus is revealed using noninvasive single-cell approaches, which ultimately lead to the resolution required for the analysis of highly controlled molecular processes taking place within live cells. We also describe the efforts being made towards physiological approaches within the context of living organisms.

A systematic analysis of disease-associated variants in the 3' regulatory regions of human protein-coding genes II: the importance of mRNA secondary structure in assessing the functionality of 3' UTR variants

In an attempt both to catalogue 3' regulatory region (3' RR)-mediated disease and to improve our understanding of the structure and function of the 3' RR, we have performed a systematic analysis of disease-associated variants in the 3' RRs of human protein-coding genes. We have previously analysed the variants that have occurred in two specific domains/motifs of the 3' untranslated region (3' UTR) as well as in the 3' flanking region. Here we have focused upon 83 known variants within the upstream sequence (USS; between the translational termination codon and the upstream core polyadenylation signal sequence) of the 3' UTR. To place these variants in their proper context, we first performed a comprehensive survey of known cis-regulatory elements within the USS and the mechanisms by which they effect post-transcriptional gene regulation. Although this survey supports the view that RNA regulatory elements function within the context of specific secondary structures, there are no general rules governing how secondary structure might exert its influence. We have therefore addressed this question by systematically evaluating both functional and non-functional (based upon in vitro reporter gene and/or electrophoretic mobility shift assay data) USS variant-containing sequences against known cis-regulatory motifs within the context of predicted RNA secondary structures. This has allowed us not only to establish a reliable and objective means to perform secondary structure prediction but also to identify consistent patterns of secondary structural change that could potentiate the discrimination of functional USS variants from their non-functional counterparts. The resulting rules were then used to infer potential functionality in the case of some of the remaining functionally uncharacterized USS variants, from their predicted secondary structures. This not only led us to identify further patterns of secondary structural change but also several potential novel cis-regulatory motifs within the 3' UTRs studied.

The living test-tube: imaging of real-time gene expression

Cells are dynamic entities. Not only are some cells motile but there is constant motion of organelles, proteins, nucleic acids and other molecules within every living cell. These complex molecular pathways control the life cycle of a cell and all come down to the basic players of the gene expression pathway: DNA, RNA and protein. It is therefore imperative to study biological processes as they naturally occur-in living cells, and to unravel the biophysical rules that govern intracellular dynamics. Towards this end, genetically encoded fluorescent proteins have become one of the major tools available for the study of kinetic processes taking place in real-time. This review will focus on the technical developments available for the study of gene activity in living cells and will summarize the novel biological information extracted from these approaches.

The retrovirus RNA trafficking granule: from birth to maturity

Post-transcriptional events in the life of an RNA including RNA processing, transport, translation and metabolism are characterized by the regulated assembly of multiple ribonucleoprotein (RNP) complexes. At each of these steps, there is the engagement and disengagement of RNA-binding proteins until the RNA reaches its final destination. For retroviral genomic RNA, the final destination is the capsid. Numerous studies have provided crucial information about these processes and serve as the basis for studies on the intracellular fate of retroviral RNA. Retroviral RNAs are like cellular mRNAs but their processing is more tightly regulated by multiple cis-acting sequences and the activities of many trans-acting proteins. This review describes the viral and cellular partners that retroviral RNA encounters during its maturation that begins in the nucleus, focusing on important events including splicing, 3' end-processing, RNA trafficking from the nucleus to the cytoplasm and finally, mechanisms that lead to its compartmentalization into progeny virions.