RNA transport to the vegetal cortex of Xenopus oocytes

Biology of primordial germ cells in vertebrates with emphasis in urodeles amphibians

Primordial germ cells (PGCs) are highly specialized cells that play a relevant role in the maintenance and evolution of the species, since they create new combinations of genetic information between the organisms. Amphibians are a class of amniote vertebrates that are divided into three subclasses, the anurans (frogs and toads), the urodeles (salamanders and newts), and the gymnophiones (caecilians). The study of PGCs in amphibians has been addressed in more detail in anurans while little is known about the biology of this cell lineage in urodeles. Studies in some urodeles species have suggested that PGCs are of mesodermal origin, specifying in the lateral plate mesoderm at the late gastrula stage. With classical experiments it shown that, there is an induction of mesoderm, therefore most likely urodeles PGCs develop from unspecialized mesodermal tissue that responds to extracellular signals. However, some fundamental biological processes of PGCs such as the analysis of their specification, arrival, and colonization to the gonads, and their maintenance and differentiation into mature and fertile gametes remain to be elucidated. Therefore, knowledge about the biology of PGCs is of great importance to ensure the perpetuation of urodeles amphibians, as some species are in danger of becoming extinct.

Specific binding of VegT mRNA localization signal to membranes in Xenopus oocytes

We have studied the interaction of a VegT mRNA localization signal sequence with the membranes of the mitochondrial cloud in Xenopus oocytes, and the binding of the VegT mRNA signal sequence to the lipid raft regions of the vesicles bounded by ordered and disordered phospholipid bilayers. RNA preference for the membranes of the mitochondrial cloud was confirmed using microscopy of a fluorescence resonance energy transfer from RNA molecules to membranes. Our studies show that VegT mRNA has a higher affinity for ordered regions of lipid bilayers. This conclusion is supported by the dissociation constant measurements for RNA-liposome complex and the visualization of the FRET signal between giant vesicles and RNA. Our data indicate that these affinities are sensitive and distinct to the location of the localization elements within the VegT mRNA localization signal structure. Therefore, specific binding of VegT mRNA localization signal sequence to membranes can be responsible for polarized distribution of VegT mRNA in Xenopus oocytes. We suggest that the mechanism of this binding can involve the interaction of the localization elements within the VegT mRNA signal sequence with lipid raft regions of the mitochondrial cloud membranes, thereby utilizing localization elements as novel lipid raft-binding RNA motifs.

Bioinformatics Approaches to Gain Insights into cis-Regulatory Motifs Involved in mRNA Localization

Messenger RNA (mRNA) is a fundamental intermediate in the expression of proteins. As an integral part of this important process, protein production can be localized by the targeting of mRNA to a specific subcellular compartment. The subcellular destination of mRNA is suggested to be governed by a region of its primary sequence or secondary structure, which consequently dictates the recruitment of trans-acting factors, such as RNA-binding proteins or regulatory RNAs, to form a messenger ribonucleoprotein particle. This molecular ensemble is requisite for precise and spatiotemporal control of gene expression. In the context of RNA localization, the description of the binding preferences of an RNA-binding protein defines a motif, and one, or more, instance of a given motif is defined as a localization element (zip code). In this chapter, we first discuss the cis-regulatory motifs previously identified as mRNA localization elements. We then describe motif representation in terms of entropy and information content and offer an overview of motif databases and search algorithms. Finally, we provide an outline of the motif topology of asymmetrically localized mRNA molecules.

Asymmetric Localization and Distribution of Factors Determining Cell Fate During Early Development of Xenopus laevis

Asymmetric division is a property of eukaryotic cells that is fundamental to the formation of higher life forms. Despite its importance, the mechanism behind it remains elusive. Asymmetry in the cell is induced by polarization of cell fate determinants that become unevenly distributed among progeny cells. So far dozens of determinants have been identified. Xenopus laevis is an ideal system to study asymmetric cell division during early development, because of the huge size of its oocytes and early-stage blastomeres. Here, we present the current knowledge about localization and distribution of cell fate determinants along the three body axes: animal-vegetal, dorsal-ventral, and left-right. Uneven distribution of cell fate determinants during early development specifies the formation of the embryonic body plan.

Maternal messages to live by: a personal historical perspective

In the 1980s, the study of localized maternal mRNAs was just emerging as a new research area. Classic embryological studies had linked the inheritance of cytoplasmic domains with specific cell lineages, but the underlying molecular nature of these putative determinants remained a mystery. The model system Xenopus would play a pivotal role in the progress of this new field. In fact, the first localized maternal mRNA to be identified and cloned from any organism was Xenopus vg1, a TGF-beta family member. This seminal finding opened the door to many subsequent studies focused on how RNAs are localized and what functions they had in development. As the field moves into the future, Xenopus remains the system of choice for studies identifying RNA/protein transport particles and maternal RNAs through RNA-sequencing.

Hermes (Rbpms) is a Critical Component of RNP Complexes that Sequester Germline RNAs during Oogenesis

The germ cell lineage in Xenopus is specified by the inheritance of germ plasm that assembles within the mitochondrial cloud or Balbiani body in stage I oocytes. Specific RNAs, such as nanos1, localize to the germ plasm. nanos1 has the essential germline function of blocking somatic gene expression and thus preventing Primordial Germ Cell (PGC) loss and sterility. Hermes/Rbpms protein and nanos RNA co-localize within germinal granules, diagnostic electron dense particles found within the germ plasm. Previous work indicates that nanos accumulates within the germ plasm through a diffusion/entrapment mechanism. Here we show that Hermes/Rbpms interacts with nanos through sequence specific RNA localization signals found in the nanos-3'UTR. Importantly, Hermes/Rbpms specifically binds nanos, but not Vg1 RNA in the nucleus of stage I oocytes. In vitro binding data show that Hermes/Rbpms requires additional factors that are present in stage I oocytes in order to bind nanos1. One such factor may be hnRNP I, identified in a yeast-2-hybrid screen as directly interacting with Hermes/Rbpms. We suggest that Hermes/Rbpms functions as part of a RNP complex in the nucleus that facilitates selection of germline RNAs for germ plasm localization. We propose that Hermes/Rbpms is required for nanos RNA to form within the germinal granules and in this way, participates in the germline specific translational repression and sequestration of nanos RNA.

Localisation of RNAs into the germ plasm of vitellogenic Xenopus oocytes

We have studied the localisation of mRNAs in full-grown Xenopus laevis oocytes by injecting fluorescent RNAs, followed by confocal microscopy of the oocyte cortex. Concentrating on RNA encoding the Xenopus Nanos homologue, nanos1 (formerly Xcat2), we find that it consistently localised into aggregated germ plasm ribonucleoprotein (RNP) particles, independently of cytoskeletal integrity. This implies that a diffusion/entrapment-mediated mechanism is active, as previously reported for previtellogenic oocytes. Sometimes this was accompanied by localisation into scattered particles of the “late”, Vg1/VegT pathway; occasionally only late pathway localisation was seen. The Xpat RNA behaved in an identical fashion and for neither RNA was the localisation changed by any culture conditions tested. The identity of the labelled RNP aggregates as definitive germ plasm was confirmed by their inclusion of abundant mitochondria and co-localisation with the germ plasm protein Hermes. Further, the nanos1/Hermes RNP particles are interspersed with those containing the germ plasm protein Xpat. These aggregates may be followed into the germ plasm of unfertilized eggs, but with a notable reduction in its quantity, both in terms of injected molecules and endogenous structures. Our results conflict with previous reports that there is no RNA localisation in large oocytes, and that during mid-oogenesis even germ plasm RNAs localise exclusively by the late pathway. We find that in mid oogenesis nanos1 RNA also localises to germ plasm but also by the late pathway. Late pathway RNAs, Vg1 and VegT, also may localise into germ plasm. Our results support the view that mechanistically the two modes of localisation are extremely similar, and that in an injection experiment RNAs might utilise either pathway, the distinction in fates being very subtle and subject to variation. We discuss these results in relation to their biological significance and the results of others.

Putting RNAs in the right place at the right time: RNA localization in the frog oocyte

Localization of maternal mRNAs in many developing organisms provides the basis for both initial polarity during oogenesis and patterning during embryogenesis. Prominent examples of this phenomenon are found in Xenopus laevis, where localized maternal mRNAs generate developmental polarity along the animal/vegetal axis. Targeting of mRNA molecules to specific subcellular regions is a fundamental mechanism for spatial regulation of gene expression, and considerable progress has been made in defining the underlying molecular pathways.

Polarizing animal cells via mRNA localization in oogenesis and early development

The localization of mRNAs in developing animal cells is essential for establishing cellular polarity and setting up the body plan for subsequent development. Cellular and molecular mechanisms by which maternal mRNAs are localized during oogenesis have been extensively studied in Drosophila and Xenopus. In contrast, evidence for mechanisms used in the localization of mRNAs encoded by developmentally important genes has also been accumulating in several other organisms. This offers the opportunity to unravel the fundamental mechanisms of mRNA localization shared among many species, as well as unique mechanisms specifically acquired or retained by animals based on their developmental needs. In addition to maternal mRNAs, the localization of zygotically expressed mRNAs in the cells of cleaving embryos is also important for early development. In this review, mRNA localization dynamics in the oocytes/eggs of Drosophila and Xenopus are first summarized, and evidence for localized mRNAs in the oocytes/eggs and cleaving embryos of other organisms is then presented.

Microtubule actin crosslinking factor 1 regulates the Balbiani body and animal-vegetal polarity of the zebrafish oocyte

Although of fundamental importance in developmental biology, the genetic basis for the symmetry breaking events that polarize the vertebrate oocyte and egg are largely unknown. In vertebrates, the first morphological asymmetry in the oocyte is the Balbiani body, a highly conserved, transient structure found in vertebrates and invertebrates including Drosophila, Xenopus, human, and mouse. We report the identification of the zebrafish magellan (mgn) mutant, which exhibits a novel enlarged Balbiani body phenotype and a disruption of oocyte polarity. To determine the molecular identity of the mgn gene, we positionally cloned the gene, employing a novel DNA capture method to target region-specific genomic DNA of 600 kb for massively parallel sequencing. Using this technique, we were able to enrich for the genomic region linked to our mutation within one week and then identify the mutation in mgn using massively parallel sequencing. This is one of the first successful uses of genomic DNA enrichment combined with massively parallel sequencing to determine the molecular identity of a gene associated with a mutant phenotype. We anticipate that the combination of these technologies will have wide applicability for the efficient identification of mutant genes in all organisms. We identified the mutation in mgn as a deletion in the coding sequence of the zebrafish microtubule actin crosslinking factor 1 (macf1) gene. macf1 is a member of the highly conserved spectraplakin family of cytoskeletal linker proteins, which play diverse roles in polarized cells such as neurons, muscle cells, and epithelial cells. In mgn mutants, the oocyte nucleus is mislocalized; and the Balbiani body, localized mRNAs, and organelles are absent from the periphery of the oocyte, consistent with a function for macf1 in nuclear anchoring and cortical localization. These data provide the first evidence for a role for spectraplakins in polarization of the vertebrate oocyte and egg.

How the axes of the embryo are established is an important question in developmental biology. In many organisms, the axes of the embryo are established during oogenesis through the generation of a polarized egg. Very little is known regarding the mechanisms of polarity establishment and maintenance in vertebrate oocytes and eggs. We have identified a zebrafish mutant called magellan, which displays a defect in egg polarity. The gene disrupted in the magellan mutant encodes the cytoskeletal linker protein microtubule actin crosslinking factor 1 (macf1). In vertebrates, it can take years to identify the molecular nature of a mutation. We used a new technique to identify the magellan mutation, which allowed us to rapidly isolate genomic DNA linked to the mutation and sequence it. Our results describe an important new function for macf1 in polarizing the oocyte and egg and demonstrate the feasibility of this new technique for the efficient identification of mutations.

Identification of vegetal RNA-localization elements in Xenopus oocytes

Localized mRNAs have been identified in a large variety of cell types where they contribute to the establishment of cell asymmetries and can function as cell fate determinants. In Xenopus, RNAs that localize to the vegetal cortex during oogenesis function in early embryonic patterning as well as in the development of primordial germ cells. Based on their temporal and spatial localization patterns, vegetally localizing RNAs are referred to as either early-pathway RNAs which transiently localize in the mitochondrial cloud, or as late-pathway RNAs. Vegetal RNA-localization is driven by cis-acting signal sequences that, in most cases, were found to reside in the 3'-UTRs and which are recognized by trans-acting localization factors. Here we describe the methods of how vegetal RNA-localization elements can be identified by injection of fluorescently-labeled or tagged RNAs.

Detection of protein-RNA complexes in Xenopus oocytes

There is a remarkable variety of mechanisms for controlling post-transcriptional gene expression that is achieved through the formation of ribonucleoprotein (RNP) complexes on specific cis-acting regions of mRNA. These complexes regulate splicing, nuclear and cytoplasmic polyadenylation, stability, localization, and translation. Thus, it is important to be able to detect the association of specific proteins with specific RNAs within the context of these RNP complexes. We describe a method to test for protein-RNA complexes in Xenopus oocytes. The procedure combines immunoprecipitation with reverse transcription-PCR (RT-PCR) and does not entail chemical or photo crosslinking. Microinjected mRNA is efficiently translated in Xenopus oocytes; thus, in cases where primary antibody is not available, an epitope-tagged version of the protein can be expressed for utilization in this procedure. The inclusion of control mRNAs has provided no evidence of nonspecific protein reassociation to RNA during or subsequent to cell lysis. The method has been used to document the association of certain trans-acting factors specifically with localized mRNAs in Xenopus oocytes.

Participation of Xenopus Elr-type proteins in vegetal mRNA localization during oogenesis

Directional transport of specific mRNAs is of primary biological relevance. In Xenopus oocytes, mRNA localization to the vegetal pole is important for germ layer formation and germ cell development. Using a biochemical approach, we identified Xenopus Elr-type proteins, homologs of the Hu/ELAV proteins, as novel components of the vegetal mRNA localization machinery. They bind specifically to the localization elements of several different vegetally localizing Xenopus mRNAs, and they are part of one RNP together with other localization proteins, such as Vg1RBP and XStaufen 1. Blocking Elr-type protein binding by either localization element mutagenesis or antisense morpholino oligonucleotide-mediated masking of their target RNA structures, as well as overexpression of wild type and mutant ElrB proteins, interferes with vegetal localization in Xenopus oocytes.

Interactions of 40LoVe within the ribonucleoprotein complex that forms on the localization element of Xenopus Vg1 mRNA

Proline rich RNA-binding protein (Prrp), which associates with mRNAs that employ the late pathway for localization in Xenopus oocytes, was used as bait in a yeast two-hybrid screen of an expression library. Several independent clones were recovered that correspond to a paralog of 40LoVe, a factor required for proper localization of Vg1 mRNA to the vegetal cortex. 40LoVe is present in at least three alternatively spliced isoforms; however, only one, corresponding to the variant identified in the two-hybrid screen, can be crosslinked to Vg1 mRNA. In vitro binding assays revealed that 40LoVe has high affinity for RNA, but exhibits little binding specificity on its own. Nonetheless, it was only found associated with localized mRNAs in oocytes. 40LoVe also interacts directly with VgRBP71 and VgRBP60/hnRNP I; it is the latter factor that likely determines the binding specificity of 40LoVe. Initially, 40LoVe binds to Vg1 mRNA in the nucleus and remains with the RNA in the cytoplasm. Immunohistochemical staining of oocytes shows that the protein is distributed between the nucleus and cytoplasm, consistent with nucleocytoplasmic shuttling activity. 40LoVe is excluded from the mitochondrial cloud, which is used by RNAs that localize through the early (METRO) pathway in stage I oocytes; nonetheless, it is associated with at least some early pathway RNAs during later stages of oogenesis. A phylogenetic analysis of 2xRBD hnRNP proteins combined with other experimental evidence suggests that 40LoVe is a distant homolog of Drosophila Squid.

RNA localization to the Balbiani body in Xenopus oocytes is regulated by the energy state of the cell and is facilitated by kinesin II

Xenopus oocytes provide an excellent model system for understanding the cis-elements and protein factors that carry out mRNA localization in vertebrate cells. More than 20 mRNAs have been identified that localize to the vegetal cortex during stages II-IV of oogenesis. The earliest localizing RNAs are presorted to a subcellular structure, the Balbiani body (also called the mitochondrial cloud in Xenopus), of stage I oocytes prior to entering the vegetal cortex. While some evidence has suggested that diffusion drives RNA localization to the Balbiani body, a role for temperature and metabolic energy in this process has not been explored. To address this issue, we developed a quantitative assay to monitor RNA localization in stage I oocytes. Here we show that the rate of RNA accumulation to the Balbiani body is highly dependent on temperature and the intracellular concentration of ATP. In fact, while ATP depletion severely impairs RNA localization, increasing the intracellular concentration of ATP by a factor of two doubles the localization rate, indicating that ATP is limiting under normal conditions. We also show that RNA localization in stage I oocytes is reduced by inhibition of kinesin II, and that the Xcat-2 RNA localization element recruits kinesin II to the Balbiani body. We conclude from these studies that the energy state of the cell regulates the rate of RNA localization to the Balbiani body and that this process, at least to some extent, involves kinesin II.

PTB/hnRNP I is required for RNP remodeling during RNA localization in Xenopus oocytes

Transport of specific mRNAs to defined regions within the cell cytoplasm is a fundamental mechanism for regulating cell and developmental polarity. In the Xenopus oocyte, Vg1 RNA is transported to the vegetal cytoplasm, where localized expression of the encoded protein is critical for embryonic polarity. The Vg1 localization pathway is directed by interactions between key motifs within Vg1 RNA and protein factors recognizing those RNA sequences. We have investigated how RNA-protein interactions could be modulated to trigger distinct steps in the localization pathway and found that the Vg1 RNP is remodeled during cytoplasmic RNA transport. Our results implicate two RNA-binding proteins with key roles in Vg1 RNA localization, PTB/hnRNP I and Vg1RBP/vera, in this process. We show that PTB/hnRNP I is required for remodeling of the interaction between Vg1 RNA and Vg1RBP/vera. Critically, mutations that block this remodeling event also eliminate vegetal localization of the RNA, suggesting that RNP remodeling is required for localization.

Orientation of microtubules suggests a role in mRNA transportation in fertilized eggs of Chinese pine (Pinus tabulaeformis)

Polysomes become associated with microtubules (MTs) in egg cells of Chinese pine upon fertilization, providing direct evidence for MT-based intracellular mRNA and polysome localization. We have investigated by immunoelectron microscopy the orientation and spatial distribution of MTs and their association with polysomes in the fertilized egg cells. There is a perinuclear accumulation of MTs and polysomes in the zygote soon after fertilization. At this time, some of the MTs are perpendicular to the nuclear envelope and directly connected to the outer membrane or nuclear-pore complexes (NPC) at one end, and the other ends reach to the outer tier or cortical MTs that are parallel to the long axis of the zygote. The polysomes in the perinuclear region show the same spatial and temporal pattern as the MTs. Immunolocalization of the mRNA-binding protein hnRNP indicates that the mRNAs are loaded onto the nucleus-associated MTs immediately after their export from the nuclear-pore complexes. The polysomes and mRNAs are then transported from these MTs to the outer tier and/or cortical MTs, where they further localize to the polar region of the cell.

The efficiency of Xenopus primordial germ cell migration depends on the germplasm mRNA encoding the PDZ domain protein Grip2

A microarray analysis of vegetal pole sequences in the egg and early Xenopus laevis embryo identified Unigene Xl.14891 as a vegetally localized RNA. Analysis of the Xenopus tropicalis genome showed this Unigene to be localized near the 3' end of the Grip2 (glutamate receptor interacting protein 2) transcription unit. RACE showed that the Unigene represented the 3' UTR of Grip2 mRNA. Grip2 mRNA is present in the mitochondrial cloud of late pre-vitellogenic oocytes and then in the germplasm through oogenesis and early development until tailbud tadpole stages. Interference with Grip2 mRNA translation using two antisense morpholino oligos (MOs) impairs primordial germ cell (PGC) migration to the germinal ridges. Both MOs also inhibit swimming movements of the tailbud tadpole, known to involve glutamate receptors. We conclude that Grip2 has several functions in the embryo, including enabling efficient PGC migration.

Transient occurrence of vasa-expressing cells in nongenital segments during embryonic development in the oligochaete annelid Tubifex tubifex

The primordial germ cells (PGCs) in the oligochaete annelid Tubifex tubifex are mesodermal in origin and are located in the two midbody segments X and XI in which the testis and the ovary are formed, respectively. To identify a molecular marker for the Tubifex PGCs, we isolated the Tubifex homologue (Ttu-vas) of the Drosophila vasa gene. Using whole-mount in situ hybridization, we examined the spatial expression patterns of Ttu-vas from one-cell stage through juvenile stage. Ttu-vas messenger ribonucleic acid (RNA) is present as a maternal transcript distributed broadly throughout the early stages. Ttu-vas is expressed in all of the early cleavage blastomeres, in which Ttu-vas RNA associates with mitotic spindles and pole plasms. Expression of Ttu-vas gradually becomes restricted, first to teloblasts, then to their blast cell progeny comprising the germ bands (GBs), and finally to a set of large ventral cells (termed VE cells) in a variable set of midbody segments including the genital segments (X and XI). At the end of embryogenesis, VE cells are confined to genital segments where they are presumably germline precursors in the juvenile. Staining with a cross-reacting anti-Vasa antibody suggested that VE cells express Ttu-vas protein to the same extent irrespective of their positions along the anteroposterior axis. A set of cell ablation experiments suggested that VE cells are derived from the mesodermal teloblast lineage and that the emergence of VE cells takes place independently of the presence of the ectodermal GBs that normally overlay the mesoderm. These results suggest that T. tubifex generates supernumerary presumptive PGCs during embryogenesis whose number is variable among embryos.

3'-UTR SIRF: a database for identifying clusters of whort interspersed repeats in 3' untranslated regions

Background

Short (~5 nucleotides) interspersed repeats regulate several aspects of post-transcriptional gene expression. Previously we developed an algorithm (REPFIND) that assigns P-values to all repeated motifs in a given nucleic acid sequence and reliably identifies clusters of short CAC-containing motifs required for mRNA localization in Xenopus oocytes.

Description

In order to facilitate the identification of genes possessing clusters of repeats that regulate post-transcriptional aspects of gene expression in mammalian genes, we used REPFIND to create a database of all repeated motifs in the 3' untranslated regions (UTR) of genes from the Mammalian Gene Collection (MGC). The MGC database includes seven vertebrate species: human, cow, rat, mouse and three non-mammalian vertebrate species. A web-based application was developed to search this database of repeated motifs to generate species-specific lists of genes containing specific classes of repeats in their 3'-UTRs. This computational tool is called 3'-UTR SIRF (Short Interspersed Repeat Finder), and it reveals that hundreds of human genes contain an abundance of short CAC-rich and CAG-rich repeats in their 3'-UTRs that are similar to those found in mRNAs localized to the neurites of neurons. We tested four candidate mRNAs for localization in rat hippocampal neurons by in situ hybridization. Our results show that two candidate CAC-rich (Syntaxin 1B and Tubulin β4) and two candidate CAG-rich (Sec61α and Syntaxin 1A) mRNAs are localized to distal neurites, whereas two control mRNAs lacking repeated motifs in their 3'-UTR remain primarily in the cell body.

Conclusion

Computational data generated with 3'-UTR SIRF indicate that hundreds of mammalian genes have an abundance of short CA-containing motifs that may direct mRNA localization in neurons. In situ hybridization shows that four candidate mRNAs are localized to distal neurites of cultured hippocampal neurons. These data suggest that short CA-containing motifs may be part of a widely utilized genetic code that regulates mRNA localization in vertebrate cells. The use of 3'-UTR SIRF to search for new classes of motifs that regulate other aspects of gene expression should yield important information in future studies addressing cis-regulatory information located in 3'-UTRs.

The mRNA coding for Xenopus glutamate receptor interacting protein 2 (XGRIP2) is maternally transcribed, transported through the late pathway and localized to the germ plasm

Using a large-scale in situ hybridization screening, we found that the mRNA coding for Xenopus glutamate receptor interacting protein 2 (XGRIP2) was localized to the germ plasm of Xenopus laevis. The mRNA is maternally transcribed in oocytes and, during maturation, transported to the vegetal germ plasm through the late pathway where VegT and Vg1 mRNAs are transported. In the 3'-untranslated region (UTR) of the mRNA, there are clusters of E2 and VM1 localization motifs that were reported to exist in the mRNAs classified as the late pathway group. With in situ hybridization to the sections of embryos, the signal could be detected in the cytoplasm of migrating presumptive primordial germ cells (pPGCs) until stage 35. At stage 40, when the cells cease to migrate and reach the dorsal mesentery, the signal disappeared. A possible role of XGRIP2 in pPGCs of Xenopus will be discussed.

Studies on TAQ1 polymorphism in the 3'untranslated region of IL-12P40 gene in HCV patients infected predominantly with genotype 3

Host immunity plays an important role in viral persistence and progression of liver disease in HCV infected patients. IL-12 induces production of IFN-gamma, a potent antiviral agent. IL-12 comprises two subunits; IL-p35 and IL-12p40, which are encoded by two different genes located on chromosome 3 and 5, respectively. Single nucleotide polymorphism at A1188C in the 3'UTR of IL-12p40 gene is associated with immune mediated diseases. Association of IL-12p40 A1188C polymorphism with the outcome of HCV infection was investigated in this study. Two hundred and fifty three histologically proven chronic hepatitis C patients (43 +/- 13 years, male:female: 185:68) and 380 matched controls were included. Genotyping was performed by RFLP and confirmed by direct sequencing. To assess correlation of immune gene polymorphism with severity of HCV-related liver disease, patients were divided into those with fibrosis score of < or = 2 (mild) or > 2 (severe), and histological activity index (HAI) of = 5 (mild) or > 5 (severe). The distribution of A/A, A/C or C/C alleles in the controls was comparable to the patients. The distribution of C/C allele was significantly more common in patients with mild as compared to severe fibrosis (23.7% vs. 6.25%, P = 0.004). No significant difference was observed for any of the genetic markers with HAI or with normal or raised alanine aminotransferase (ALT). These results show that the C/C allele of IL-12p40 gene could render genetic protection against development of severe liver disease in patients infected with HCV.

Xenopus Xpat protein is a major component of germ plasm and may function in its organisation and positioning

In many animals, including Drosophila, C. elegans, zebrafish and Xenopus, the germ line is specified by maternal determinants localised in a distinct cytoplasmic structure called the germ plasm. This is consists of dense granules, mitochondria, and specific localised RNAs. We have characterised the expression and properties of the protein encoded by Xpat, an RNA localised to the germ plasm of Xenopus. Immunofluorescence and immunoblotting showed that this novel protein is itself a major constituent of germ plasm throughout oogenesis and early development, although it is also present in other regions of oocytes and embryos, including their nuclei. We found that an Xpat-GFP fusion protein can localise correctly in cultured oocytes, in early oocytes to the 'mitochondrial cloud', from which germ plasm originates, and in later oocytes to the vegetal cortex. The localisation process was microtubule-dependent, while cortical anchoring required microfilaments. Xpat-GFP expressed in late stage oocytes assembled into circular fields of multi-particulate structures resembling endogenous fields of germ plasm islands. Furthermore these structures could be induced to form at ectopic sites by manipulation of culture conditions. Ectopic Xpat-GFP islands were able to recruit mitochondria, a major germ plasm component. These data suggest that Xpat protein has an important role in Xenopus germ plasm formation, positioning and maintenance.

Evidence for common machinery utilized by the early and late RNA localization pathways in Xenopus oocytes

In Xenopus, an early and a late pathway exist for the selective localization of RNAs to the vegetal cortex during oogenesis. Previous work has suggested that distinct cellular mechanisms mediate localization during these pathways. Here, we provide several independent lines of evidence supporting the existence of common machinery for RNA localization during the early and late pathways. Data from RNA microinjection assays show that early and late pathway RNAs compete for common localization factors in vivo, and that the same short RNA sequence motifs are required for localization during both pathways. In addition, quantitative filter binding assays demonstrate that the late localization factor Vg RBP/Vera binds specifically to several early pathway RNA localization elements. Finally, confocal imaging shows that early pathway RNAs associate with a perinuclear microtubule network that connects to the mitochondrial cloud of stage I oocytes suggesting that motor driven transport plays a role during the early pathway as it does during the late pathway. Taken together, our data indicate that common machinery functions during the early and late pathways. Thus, RNA localization to the vegetal cortex may be a regulated process such that differential interactions with basal factors determine when distinct RNAs are localized during oogenesis.

RNA localization mechanisms in oocytes

In many animals, normal development depends on the asymmetric distribution of maternal determinants, including various coding and noncoding RNAs, within the oocyte. The temporal and spatial distribution of localized RNAs is determined by intricate mechanisms that regulate their movement and anchoring. These mechanisms involve cis-acting sequences within the RNA molecules and a multitude of trans-acting factors, as well as a polarized cytoskeleton, molecular motors and specific transporting organelles. The latest studies show that the fates of localized RNAs within the oocyte cytoplasm are predetermined in the nucleus and that nuclear proteins, some of them deposited on RNAs during splicing, together with the components of the RNA-silencing pathway, dictate the proper movement, targeting, anchoring and translatability of localized RNAs.

Evidence for overlapping, but not identical, protein machineries operating in vegetal RNA localization along early and late pathways in Xenopus oocytes

RNAs that localize to the vegetal cortex of Xenopus oocytes are involved in early embryonic patterning and cell fate specification. Two mechanistically distinct pathways lead to RNA enrichment at the vegetal cortex: the early and the late. While several candidate proteins that seem to operate in the late localization pathway have been identified, proteins involved in the early pathway remain to be identified. In this study, we report on the isolation of a novel vegetally localized RNA in Xenopus oocytes that makes use of the early pathway and encodes a protein with a conserved but functionally uncharacterized NIF-motif. The localization signal of XNIF was mapped to a 300-nucleotide region in the 5'-UTR, which is able to mediate both accumulation to the mitochondrial cloud in stage I oocytes, as well as vegetal transport in later stage oocytes. The XNIF-LE contains 16 copies of the previously defined CAC-containing signal motifs for RNA localization. A critical number of such repeats seems to be required for accumulation in the mitochondrial cloud along the early pathway, but additional repeats seem to be required for localization along the late pathway. Cross-linking experiments identify two novel proteins of 62 and 64 kDa that interact with the XNIF-LE but not with the Vg1-LE that operates in the late pathway. Conversely, at least two of the previously identified VgRBPs, Vg1RBP1 and Prrp, also bind to the XNIF-LE. Thus, overlapping, but not identical, protein machineries mediate vegetal RNA localization along early and late pathways in Xenopus oocytes.

Localization of RNAs to the mitochondrial cloud in Xenopus oocytes through entrapment and association with endoplasmic reticulum

The germ cell lineage in Xenopus is specified by the inheritance of germ plasm, which originates within a distinct "mitochondrial cloud" (MC) in previtellogenic oocytes. Germ plasm contains localized RNAs implicated in germ cell development, including Xcat2 and Xdazl. To understand the mechanism of the early pathway through which RNAs localize to the MC, we applied live confocal imaging and photobleaching analysis to oocytes microinjected with fluorescent Xcat2 and Xdazl RNA constructs. These RNAs dispersed evenly throughout the cytoplasm through diffusion and then became progressively immobilized and formed aggregates in the MC. Entrapment in the MC was not prevented by microtubule disruption and did not require localization to germinal granules. Immobilized RNA constructs codistributed and showed coordinated movement with densely packed endoplasmic reticulum (ER) concentrated in the MC, as revealed with Dil16(3) labeling and immunofluorescence analysis. Vg1RBP/Vera protein, which has been implicated in linking late pathway RNAs to vegetal ER, was shown to bind specifically both wild-type Xcat2 3' untranslated region and localization-defective constructs. We found endogenous Vg1RBP/Vera and Vg1RBP/Vera-green fluorescent protein to be largely excluded from the MC but subsequently to codistribute with Xcat2 and ER at the vegetal cortex. We conclude that germ line RNAs localize into the MC through a diffusion/entrapment mechanism involving Vg1RBP/Vera-independent association with ER.

Xvelo1 uses a novel 75-nucleotide signal sequence that drives vegetal localization along the late pathway in Xenopus oocytes

Vegetally localized RNAs in Xenopus laevis oocytes are involved in the patterning of the early embryo as well as in cell fate specification. Here we report on the isolation and characterization of a novel, vegetally localized RNA in Xenopus oocytes termed Xvelo1. It encodes a protein of unknown biological function and it represents an antisense RNA for XPc1 over a length of more than 1.8 kb. Xvelo1 exhibits a localization pattern reminiscent of the late pathway RNAs Vg1 and VegT; it contains RNA localization elements (LE) which do not match with the consensus structural features as deduced from Vg1 and VegT LEs. Nevertheless, the protein binding pattern as observed for Xvelo1-LE in UV cross-linking experiments and coimmunoprecipitation assays is largely overlapping with the one obtained for Vg1-LE. These observations suggest that the structural features recognized by the protein machinery that drives localization of maternal mRNAs along the late pathway in Xenopus oocytes must be redefined.

Kinesin II Mediates Vg1 mRNA Transport in Xenopus Oocytes

The subcellular localization of specific mRNAs is a widespread mechanism for regulating gene expression. In Xenopus oocytes microtubules are required for localization of Vg1 mRNA to the vegetal cortex during the late RNA localization pathway. The factors that mediate microtubule-based RNA transport during the late pathway have been elusive. Here we show that heterotrimeric kinesin II becomes enriched at the vegetal cortex of stage III/IV Xenopus oocytes concomitant with the localization of endogenous Vg1 mRNA. In addition, expression of a dominant negative mutant peptide fragment or injection of a function-blocking antibody, both of which impair the function of heterotrimeric kinesin II, block localization of Vg1 mRNA. We also show that exogenous Vg1 RNA or Xcat-2, another RNA that can use the late pathway, recruits endogenous kinesin II to the vegetal pole and colocalizes with it at the cortex. These data support a model in which kinesin II mediates the transport of specific RNA complexes destined for the vegetal cortex.

Identification and characterization of the Xlsirt cis-acting RNA localization element

There are many RNAs that are localized to the vegetal cortex of Xenopus laevis oocytes. One family of localized transcripts, Xlsirts (Xenopus laevis short interspersed repeat transcripts), are defined by the presence of non-coding repeat units 79-81 nucleotides long. Endogenous Xlsirt RNAs are localized through the METRO (message transport organizer) pathway that localizes RNAs during stages I and II of oogenesis. Interestingly, exogenous Xlsirt RNAs that are injected into oocytes can utilize both the METRO pathway as well as the Late pathway, which localizes RNAs during the late stages of oogenesis (stages III-VI). In all cases thus far analyzed, the localization process relies on the presence of cis-acting elements on the transcripts that are responsible for directing localization. To better understand the mechanism responsible for the use of the METRO and Late localization pathways, we sought to identify pathway-specific cis-acting localization elements contained in Xlsirts. The results showed that an intact 137 nucleotide element was necessary and sufficient to localize RNAs through the METRO and Late pathways. Further analysis of this element identified putative METRO and Late pathway localization sub-elements. Computer analysis relates the secondary structure of the 137 nt element to its ability to function as a localization element.

Xenopus Germes encodes a novel germ plasm-associated transcript

A cDNA tag specific for the vegetal pole of early Xenopus embryo was used to isolate a novel cDNA using RACE technique. The corresponding mRNA demonstrated a localization pattern typical for the germ plasm-associated messages, and was, therefore, named Germes. The open reading frame of Germes encodes a predicted 68 kDa protein with two leucine zipper motifs and a putative EF-hand domain, but otherwise no substantial homology to known proteins. In situ hybridization analysis shows that Germes transcript localizes to the vegetal cortex via the mitochondrial cloud early in oogenesis and segregates with the germ plasm during early embryogenesis. Our data indicate that Germes is a novel germ plasm-specific RNA.

Conservation of a Pumilio-Nanos complex from Drosophila germ plasm to human germ cells

Germ cells are the cells which ultimately give rise to mature sperm and eggs. In model organisms such as flies and worms, several genes that are required for formation and maintenance of germ cells have been identified and their interactions are rapidly being delineated. By contrast, little is known of the genes required for development of human germ cells and it is not clear whether findings from model organisms will translate into knowledge of human germ cell development, especially given observations that reproductive pathways may evolve more rapidly than somatic pathways. The Pumilio and Nanos genes have been especially well-characterized in model organisms and encode proteins that interact and are required for development of germ stem cells in one or both sexes. Here we report the first characterization of a mammalian Nanos homolog, human NANOS1 ( NOS1). We show that human NOS1 protein interacts with the human PUMILIO-2 (PUM2) protein via highly conserved domains to form a stable complex. We also show that in men, the NOS1 and PUM2 proteins are particularly abundant in germline stem cells. These observations mirror those in distant species and document for the first time a conserved protein-protein interaction in germ cells from flies to humans. These results suggest the possibility that the interaction of PUM2 and NOS1 may play a conserved role in germ cell development and maintenance in humans as in model organisms.

A homolog of FBP2/KSRP binds to localized mRNAs in Xenopus oocytes

A Xenopus oocyte expression library was screened for proteins that bind to the 340-nucleotide localization element of Vg1 mRNA. Four different isolates encoded a Xenopus homolog of the human transcription factor, FUSE-binding protein 2 (FBP2). This protein has been independently identified as the splicing regulatory factor KSRP. The only significant difference between the Xenopus protein, designated VgRBP71, and KSRP is the absence of a 58 amino acid segment near the N-terminal of the former. In vivo binding assays show that VgRBP71 is associated with mRNAs localized to either the vegetal or animal hemispheres, but was not found with control mRNAs. Unlike other factors that bind to the localization element of Vg1 mRNA, VgRBP71 does not accumulate at the vegetal cortex with the mRNA; rather, it is present in the nucleus and throughout the cytoplasm at all stages of oogenesis. Cytoplasmic VgRBP71 appears to be most concentrated at the cell cortex. VgRBP71 interacts with Prrp, another protein that binds to the Vg1 localization element; this association does not require the presence of Vg1 mRNA.

A ubiquitous and conserved signal for RNA localization in chordates

During oogenesis in Xenopus laevis, several RNAs that localize to the vegetal cortex via one of three temporally defined pathways have been identified. Although individual mRNAs utilize only one pathway, there is functional overlap and apparent continuity between them, suggesting that common cis-acting sequences may exist. Because previous work with the Vg1 mRNA revealed that short nontandem repeats are important for localization, we developed a new computer program, called REPFIND, to expedite the identification of repeated motifs in other localized RNAs. Here we show that clusters of short CAC-containing motifs characterize the localization elements (LEs) of virtually all mRNAs localized to the vegetal cortex of Xenopus oocytes. A search for this signal in GenBank [9] resulted in the identification of new localized mRNAs, demonstrating the applicability of REPFIND to predict localized RNAs. CAC-rich LEs are also found in ascidians and other vertebrates, indicating that these cis regulatory elements are conserved in chordates. Interestingly, biochemical evidence shows that distinct CAC-containing motifs have different functions in the localization process. Thus, clusters of CAC-containing motifs are a ubiquitous signal for RNA localization and can signal localization in a variety of pathways through slight variations in sequence composition.

An evolutionary conserved region in the vasa 3'UTR targets RNA translation to the germ cells in the zebrafish

BACKGROUND

In many animals, germ cells are set aside from somatic cells early during development to give rise to sperm in males and eggs in females. One strategy to achieve this separation is to localize special cytoplasmic granules to the precursors of the germline. In Drosophila, the vasa gene has been shown to encode an essential component of these granules. While Vasa protein is directly targeted to the forming germ cells of Drosophila, Vasa protein expression in the germline of Xenopus and zebrafish is thought to be achieved by RNA localization.

RESULTS

To analyze whether the machinery responsible for RNA localization is conserved among lower vertebrates, we tested different vasa homologs for their ability to localize in Xenopus oocytes. Reporter transcripts fused to the vasa 3'UTR of zebrafish are recruited to the germ plasm of injected Xenopus oocytes, although the 3'UTR shows no clear sequence similarity to the Xenopus vasa-like DEADsouth 3'UTR. However, isolation, expression pattern analysis, and sequence inspection of vasa genes from different teleosts indicate that RNA localization correlates with the presence of several conserved regions in the 3'UTR. Introduction of reporter transcripts fused to different vasa 3'UTR deletions into Xenopus and zebrafish demonstrates that one of these conserved regions is sufficient for RNA localization in either species. Moreover, these regions target GFP translation to the germline of transgenic fish.

CONCLUSIONS

Our results suggest the existence of a common RNA localization machinery in lower vertebrates that uses a functionally conserved localization signal to target gene expression to the germline.

Vegetal localization of maternal mRNAs is disrupted by VegT depletion

VegT is an essential maternal regulator of germ layer specification in Xenopus. The localization of VegT mRNA to the vegetal cortex of the oocyte during oogenesis ensures its inheritance by vegetal and not animal cells, and directs the differentiation of vegetal cells into endoderm. Similarly localized mRNAs, Vg1 and Bicaudal-C, are also inherited by vegetal cells, while germ plasm-associated mRNAs, such as Xcat2, become incorporated into vegetally derived primordial germ cells. Although mRNA localization is clearly important for tissue specification, the mechanism of mRNA anchoring to the oocyte vegetal cortex is not understood. Here, we examine the role of VegT in cortical localization. We report that depletion of VegT mRNA caused the release of Vg1 mRNA from the vegetal cortex and a reduction of Vg1 protein, without affecting the total amount of Vg1 transcript. Furthermore, we found that Bicaudal-C and Wnt11 mRNAs were also dispersed, but not degraded, by VegT depletion, while the localization of Xcat2 and Xotx1 mRNAs was unaffected. This effect was specific to the loss of VegT mRNA and not VegT protein, since a morpholino oligo against VegT, that blocked translation without degrading mRNA, did not disperse the vegetally localized mRNAs. Therefore, a subset of localized mRNAs is dependent on VegT mRNA for anchoring to the vegetal cortex, indicating a novel function for maternal VegT mRNA.

Biochemical characterization of a cellular structure retaining vegetally localized RNAs in Xenopus late stage oocytes

Two pathways operate during Xenopus oogenesis to localize a small number of RNAs to the vegetal cortex. Correct localization of these RNAs is essential to normal development as the proteins they encode are involved in specifying cell type and in patterning the early embryo. Binding these RNAs to the vegetal cortex and thus preserving their localized condition is a critical step, although little is known about how this is achieved. In this study, we have used a biochemical approach to examine the anchoring step. Xlsirts, an abundant localized RNA (locRNA), was selectively enriched in a detergent-insoluble fraction (DIF) prepared from oocytes that had completed the RNA localization process. These putative RNA-anchoring complexes were analyzed by density gradient centrifugation and in RNA-protein binding assays. Cortical Xlsirts and other localized RNAs are specifically found in the heavy region of sucrose gradients and in the pellet, quite different from other cellular RNPs. Four proteins were identified by UV-crosslinking that bound the Xlsirts localization signal in the cortex, but not in the soluble fraction. These are likely members of the anchoring complex and appear to include vera, a characterized Vg1 RNA binding protein. Vera was found to co-sediment with other locRNAs found in the vegetal cortex, suggesting that it is a common component of locRNPs. Finally, we found that locRNPs extracted into the soluble fraction had the same buoyant density as typical ooplasmic RNPs. We propose that locRNAs are organized and anchored in the cortex as typical RNPs.

RNA anchoring in the vegetal cortex of the Xenopus oocyte

The body plan of the embryo is established by a polarized source of developmental information in the oocyte. The Xenopus laevis oocyte creates polarity by anchoring mRNAs in the vegetal cortex, including Vg1 and Xwnt-11, which might function in body plan specification, and Xcat-2, which might function in germ cell development. To identify components of the RNA anchoring mechanism, we used the manually isolated vegetal cortex (IVC) to assay loss or change in spatial arrangement of mRNAs caused by disruption of cortical elements. The role of cytoskeleton in mRNA anchoring was tested by treating oocytes with inhibitors that selectively disrupted actin microfilaments and cytokeratin filaments. Treatment of oocytes with cytochalasin B caused clumping of Vg1 and Xwnt-11 as revealed by in situ hybridization of the IVC, but did not cause their release, as confirmed by RT-PCR analysis. These mRNA clumps did not match the distribution of actin microfilament clumps, but were distributed similarly to the remnant cytokeratin filaments. Treatment of oocytes with monoclonal anti-cytokeratin antibody C11 released these mRNAs from the cortex. C11 altered the texture of the cytokeratin network, but did not affect the actin meshwork. These results show that Vg1 and Xwnt-11 are retained by a cytokeratin filament-dependent mechanism, and that organization of the cytokeratin network depend on an intact actin meshwork. Colcemid did not disrupt Vg1 and Xwnt-11 retention in the IVC, so anchoring of these mRNAs are independent of microtubules. Membrane disruption in the IVC by Triton X-100 decreased Vg1 and Xwnt-11. Loss of these mRNAs was due mainly to ribonuclease activity released from membrane components. However, when ribonuclease activity was suppressed under cold temperature, a higher amount of Vg1 and Xwnt-11 was recovered in the supernatant. This result suggested that a fraction of these mRNAs required membranes to be retained in the cortex. By contrast, Xcat-2 mRNA was neither released nor degraded following treatments with cytochalasin B, C11, colcemid and Triton X-100 under cold temperature, so no cortical element could be implicated in its anchoring.

Defining cis-acting elements and trans-acting factors in RNA localization

Research over the last 10 to 15 years has revealed that intracellular RNA localization is a widespread phenomenon found in a large range of different cell types in an equally impressive number of different organisms (Bashirullah et al., 1998; St. Johnston, 1995). Efforts have focused both on the molecular mechanisms involved in localizing RNAs to particular intracellular targets and on the functional importance (to the cell) of placing certain RNAs at particular cellular sites. In many cases, an understanding of the role of RNA localization seems to be predicated on a careful analysis of how a particular RNA achieves its characteristic distribution. A generalized model of RNA localization usually invokes cellular factors recognizing RNA target sequences. This review will focus on several systems in which cis-acting elements and trans-acting factors recognizing these elements are involved in RNA localization: how they have been defined, how they relate to each other, and how they interact and function to help achieve defined intracellular localization. Conservation of both RNA elements and protein factors across species suggests that RNA localization is probably a fundamental cellular process.

RNA localization and germ cell determination in Xenopus

In many organisms the proper development of the embryo depends on the asymmetrical distribution of maternal RNAs and proteins in the egg. Although the Xenopus oocyte is radially symmetrical it contains distinct populations of maternal RNAs that are localized either in the animal or vegetal pole. The process of localization of RNAs in Xenopus oocytes occurs during the long period of oocyte differentiation and growth that is accompanied by the elaboration of oocyte polarity. Some of the vegetally localized RNAs, such as Vg1, VegT, and Xwnt11, are involved in axial patterning and germ layer specification. Others, such as Xdazl and Xcat2, which are located in the germ plasm, are likely to play a role in the specification of germ cell fate. We will discuss the different aspects of RNA localization in Xenopus in the context of the differentiation of the germ cells and the development of the oocyte polarity.

The targeting of Xcat2 mRNA to the germinal granules depends on a cis-acting germinal granule localization element within the 3'UTR

The germ cell lineage is specified by the germ plasm, which in Xenopus laevis contains putative determinants called germinal granules. The pathway through which these structures form and how their components are assembled remain unclear. Using a combination of electron microscopy and in situ hybridization with the germinal granule-associated Xcat2 mRNA we demonstrated that the granules were derived from a branching network of granulofibrillar material within the mitochondrial cloud. Targeting of Xcat2 mRNA to the germinal granules depended on a 164-nt 3'UTR germinal granule localization element (GGLE; nt 631-795) that was distinct from the previously defined mitochondrial cloud localization element (MCLE; nt 403-630; Y. Zhou and M. L. King, 1996, Development 122, 2947-2953). This demonstrated that the Xcat 3'UTR contains a compound localization element consisting of a general element (MCLE) targeting the RNA to the mitochondrial cloud and a second element (GGLE) responsible for targeting to the germinal granules within the cloud. The GGLE when fused to Xlsirt RNA was sufficient to target this nongranule mitochondrial cloud-associated RNA to the germinal granules. This is the first example of a localization element involved in targeting an mRNA to a specific subcellular target such as the germinal granules and suggests that cis-acting elements on RNAs play an important role in the assembly of germinal granules and, therefore, the establishment of the germ cell lineage.

fatvg encodes a new localized RNA that uses a 25-nucleotide element (FVLE1) to localize to the vegetal cortex of Xenopus oocytes

Vegetally localized transcripts have been implicated in a number of important biological functions, including cell fate determination and embryonic patterning. We have isolated a cDNA, fatvg, which encodes a localized maternal transcript that exhibits a localization pattern reminiscent of Vg1 mRNA. fatvg is the homologue of a mammalian gene expressed in adipose tissues. The fatvg transcript, unlike Vg1 which localizes strictly through the Late pathway, also associates with the mitochondrial cloud that is characteristic of the METRO or Early pathway. This suggests that fatvg mRNA may utilize both the METRO and Late pathways to localize to the vegetal cortex during oogenesis. We have dissected the cis-acting localization elements of fatvg mRNA and compared these elements with Vg1 mRNA. Our results indicate that, like most localized RNAs, in a variety of systems, transcripts of fatvg contain localization elements in the 3′UTR. The 3′UTR of fatvg mRNA contains multiple elements that are able to function independently; however, it functions most efficiently when all of the elements are present. We have defined a short 25-nucleotide element that can direct vegetal localization as a single copy. This element differs in sequence from previously described Vg1 localization elements, suggesting that different localization elements are involved in the localization of RNAs through the Late pathway.

Microtubules in Xenopus oocytes are oriented with their minus-ends towards the cortex

Despite lacking centrosomes, stage VI Xenopus oocytes contain extensive networks of cytoplasmic microtubules (MTs). To gain additional insight into the factors regulating MT organization during oogenesis, we have used electron microscopy and "hook decoration" to examine the distribution and orientation of MTs in Xenopus oocytes. A limited survey of two "undecorated" stage VI oocytes revealed 218 MTs in images covering approximately 2,500 microm(2), and indicated that the MT number density of the animal cytoplasm was greater than that of the vegetal cytoplasm. Examination of five "decorated" stage VI oocytes (three animal and five vegetal hemispheres) revealed 653 MTs. Of these, 76% could be scored as having exclusively counterclockwise (CCW) or clockwise (CW) hooks. In the animal hemispheres, 93% of the scored MTs exhibited CCW hooks when viewed from the direction of the cortex, indicating that most MTs were oriented with their minus-ends out. MT orientation appeared relatively uniform throughout the animal cytoplasm: more than 90% of the scored MTs in the cortical (90%), subcortical (96%), or perinuclear (98%) cytoplasm were oriented with their minus-ends out. In the vegetal hemispheres, approximately 80% of the scored MTs exhibited CCW hooks, and thus were oriented with their minus-ends out; 96% of the scored MTs in stage III oocytes were oriented minus-end out. These observations support a model in which the cortex plays a significant role in MT nucleation and organization in Xenopus oocytes, and have significant implications for the MT-dependent transport and localization of cytoplasmic organelles and RNAs during oogenesis.

Polarizing genetic information in the egg: RNA localization in the frog oocyte

RNA localization is a powerful strategy used by cells to localize proteins to subcellular domains and to control protein synthesis regionally. In germ cells, RNA targeting has profound implications for development, setting up polarities in genetic information that drive cell fate during embryogenesis. The frog oocyte offers a useful system for studying the mechanism of RNA localization. Here, we discuss critically the process of RNA localization during frog oogenesis. Three major pathways have been identified that are temporally and spatially separated in oogenesis. Each pathway uses a different mechanism to effect RNA localization. In some cases, localization elements within the 3' untranslated region have been identified and have provided unique insights into the localization process. This important field is still in its infancy, however, and much remains to be learned.