Controlling the Messenger: Regulated Translation of Maternal mRNAs in Xenopus laevis Development

The midbody component Prc1-like is required for microtubule reorganization during cytokinesis and dorsal determinant segregation in the early zebrafish embryo

We show that the zebrafish maternal-effect mutation too much information (tmi) corresponds to zebrafish prc1-like (prc1l), which encodes a member of the MAP65/Ase1/PRC1 family of microtubule-associated proteins. Embryos from tmi homozygous mutant mothers display cytokinesis defects in meiotic and mitotic divisions in the early embryo, indicating that Prc1l has a role in midbody formation during cell division at the egg-to-embryo transition. Unexpectedly, maternal Prc1l function is also essential for the reorganization of vegetal pole microtubules required for the segregation of dorsal determinants. Whereas Prc1 is widely regarded to crosslink microtubules in an antiparallel conformation, our studies provide evidence for an additional function of Prc1l in the bundling of parallel microtubules in the vegetal cortex of the early embryo during cortical rotation and prior to mitotic cycling. These findings highlight common yet distinct aspects of microtubule reorganization that occur during the egg-to-embryo transition, driven by maternal product for the midbody component Prc1l and required for embryonic cell division and pattern formation.

TurboID functions as an efficient biotin ligase for BioID applications in Xenopus embryos

BioID is a proximity labeling strategy whose goal is to identify in vivo protein-protein interactions. The central components of this strategy are modified biotin ligase enzymes that promiscuously add biotin groups to proteins in close proximity. The transferred biotin group provides a powerful tag for purification and thus identification of interacting proteins. While a variety of modified biotin ligases were created for BioID, the original enzymes were inefficient, required long incubation times, and high intracellular biotin concentrations for protein labeling. These limitations hinder the application of BioID in contexts such as developing embryos where processes such as cell division and cell fate decisions occur rapidly. Recently, a new biotin ligase called TurboID was developed that addressed many of the deficiencies of previous enzymes. In this paper we compare TurboID to the BioID2 biotin ligase in developing Xenopus embryos. We find that the TurboID enzyme has several advantages over the BioID2 enzyme. TurboID labels proteins efficiently without the addition of additional biotin and occurs at a range of temperatures compatible with the culturing of Xenopus embryos. Biotinylation events occurred rapidly and were limited by TurboID expression and not its activity. Thus, TurboID is an efficient tool for BioID applications in Xenopus embryos and its use should facilitate the identification of interacting proteins in specific networks and complexes during Xenopus development.

Bicaudal-C Post-transcriptional regulator of cell fates and functions

Bicaudal-C (Bicc1) is an evolutionarily conserved RNA binding protein that functions in a regulatory capacity in a variety of contexts. It was originally identified as a genetic locus in Drosophila that when disrupted resulted in radical changes in early development. In the most extreme phenotypes embryos carrying mutations developed with mirror image duplications of posterior structures and it was this striking phenotype that was responsible for the name Bicaudal. These seminal studies established Bicc1 as an important regulator of Drosophila development. What was not anticipated from the early work, but was revealed subsequently in many different organisms was the broad fundamental impact that Bicc1 proteins have on developmental biology; from regulating cell fates in vertebrate embryos to defects associated with several human disease states. In the following review we present a perspective of Bicc1 focusing primarily on the molecular aspects of its RNA metabolism functions in vertebrate embryos.

mRNPs: Structure and role in development

In eukaryotic cells, mRNA molecules are coated with numerous RNA-binding proteins and so exist in ribonucleoproteins (mRNPs). The proteins associated with the mRNA regulate the fate of mRNA, including its localization, translation and decay. Before activation of translation, the mRNA does not display any template functions-it is masked. The coordinated activity of certain RNA-binding proteins determines the future fate of each mRNA individually. In embryo development, the temporal and spatial regulation of translation can cause a situation when the mRNA and the encoded protein are localized in different compartments and so the differentiation of the cells can be determined. The fundamentals of regulation of the mRNAs fate and functioning in nerves are similar to those already described for oo- and embryogenesis. Disorders in the mRNA masking and demasking result in the emergence of various diseases, in particular cancers and neuro-degenerative diseases.

Evolution and new frontiers of histology in bio-medical research

Histology refers to the study of the morphology of cells within their natural tissue environment. As a bio-medical discipline, it dates back to the development of first microscopes which allowed to override the physical visual limitation of the human eye. Since the first observations, it was understood that cell shape predicts function and, therefore, shape alterations can identify and explain dysfunction and diseases. The advancements in morphological investigation techniques have allowed to extend our understanding of the shape-function relationships close to the molecular level of organization of tissues, as well as to derive reliable data not only from fixed, and hence static, biological samples but also living cells and tissues and even for extended time periods. These modern approaches, which encompass quantitative microscopy, precision microscopy, and dynamic microscopy, represent the new frontier of morphology. This article summarizes how the microscopy techniques have evolved to properly face the challenges of biomedical sciences, thus transforming histology from a merely qualitative discipline, which played an ancillary role to traditional "major" sciences such as anatomy, to a modern experimental science capable of driving knowledge progress in biology and medicine.

A systematic, label-free method for identifying RNA-associated proteins in vivo provides insights into vertebrate ciliary beating machinery

Cell-type specific RNA-associated proteins are essential for development and homeostasis in animals. Despite a massive recent effort to systematically identify RNA-associated proteins, we currently have few comprehensive rosters of cell-type specific RNA-associated proteins in vertebrate tissues. Here, we demonstrate the feasibility of determining the RNA-associated proteome of a defined vertebrate embryonic tissue using DIF-FRAC, a systematic and universal (i.e., label-free) method. Application of DIF-FRAC to cultured tissue explants of Xenopus mucociliary epithelium identified dozens of known RNA-associated proteins as expected, but also several novel RNA-associated proteins, including proteins related to assembly of the mitotic spindle and regulation of ciliary beating. In particular, we show that the inner dynein arm tether Cfap44 is an RNA-associated protein that localizes not only to axonemes, but also to liquid-like organelles in the cytoplasm called DynAPs. This result led us to discover that DynAPs are generally enriched for RNA. Together, these data provide a useful resource for a deeper understanding of mucociliary epithelia and demonstrate that DIF-FRAC will be broadly applicable for systematic identification of RNA-associated proteins from embryonic tissues.

Maternal control of early patterning in sea urchin embryos

Sea urchin development has been studied extensively for more than a century and considered regulative since the first experimental evidence. Further investigations have repeatedly supported this standpoint by revealing the presence of inductive mechanisms that alter cell fate decisions at early cleavage stages and flexibility of development in response to environmental conditions. Some features indicate that sea urchin development is not completely regulative, but actually includes determinative events. In 16-cell embryos, mesomeres and macromeres represent multipotency, while the cell fate of most vegetal micromeres is restricted. It is known that the mature sea urchin eggs are polarized by the asymmetrical distribution of some maternal mRNAs and proteins. Spatially-distributed maternal factors are necessary for the orientation of the primary animal-vegetal axis, which is established by both maternal and zygotic mechanisms later in development. The secondary dorsal-ventral axis is conditionally specified later in development. Dorsal-ventral polarity is very liable during the early cleavages, though more recent data argue that its direction may be oriented by maternal asymmetry. In this review, we focus on the role of maternal factors in initial embryonic patterning during the first cleavages of sea urchin embryos before activation of the embryonic genome.

Cell-Cycle-Dependent Regulation of Translation: New Interpretations of Old Observations in Light of New Approaches

It is a long-standing view that global translation varies during the cell cycle and is much lower in mitosis than in other cell-cycle phases. However, the central papers in the literature are not in agreement about the extent of downregulation in mitosis, ranging from a dramatic decrease to only a marginal reduction. Herein, it is argued that the discrepancy derives from technical challenges. Cell-cycle-dependent variations are most conveniently studied in synchronized cells, but the synchronization methods by themselves often evoke stress responses that, in turn, affect translation rates. Further, it is argued that previously reported cell-cycle-dependent changes in the global translation rate to a large extent reflect responses to the synchronization methods. Recent findings strongly suggest that the global translation rate is not regulated in a cell-cycle-dependent manner. Novel techniques allowing a genome-wide analysis of translational profiles suggest that the extent and importance of selective translational regulation associated with cell-cycle transitions have been underestimated. Therefore, the main question is which messenger RNAs (mRNAs) are translated, rather than whether the global translation rate is decreased.

Primary transcripts: From the discovery of RNA processing to current concepts of gene expression - Review

The main purpose of this review is to recall for investigators - and in particular students -, some of the early data and concepts in molecular genetics and biology that are rarely cited in the current literature and are thus invariably overlooked. There is a growing tendency among editors and reviewers to consider that only data produced in the last 10-20 years or so are pertinent. However this is not the case. In exact science, sound data and lucid interpretation never become obsolete, and even if forgotten, will resurface sooner or later. In the field of gene expression, covered in the present review, recent post-genomic data have indeed confirmed many of the earlier results and concepts developed in the mid-seventies, well before the start of the recombinant DNA revolution. Human brains and even the most powerful computers, have difficulty in handling and making sense of the overwhelming flow of data generated by recent high-throughput technologies. This was easier when low throughput, more integrative methods based on biochemistry and microscopy dominated biological research. Nowadays, the need for organising concepts is ever more important, otherwise the mass of available data can generate only "building ruins" - the bricks without an architect. Concepts such as pervasive transcription of genomes, large genomic domains, full domain transcripts (FDTs) up to 100 kb long, the prevalence of post-transcriptional events in regulating eukaryotic gene expression, and the 3D-genome architecture, were all developed and discussed before 1990, and are only now coming back into vogue. Thus, to review the impact of earlier concepts on later developments in the field, I will confront former and current data and ideas, including a discussion of old and new methods. Whenever useful, I shall first briefly report post-genomic developments before addressing former results and interpretations. Equally important, some of the terms often used sloppily in scientific discussions will be clearly defined. As a basis for the ensuing discussion, some of the issues and facts related to eukaryotic gene expression will first be introduced. In chapter 2 the evolution in perception of biology over the last 60 years and the impact of the recombinant DNA revolution will be considered. Then, in chapter 3 data and theory concerning the genome, gene expression and genetics will be reviewed. The experimental and theoretical definition of the gene will be discussed before considering the 3 different types of genetic information - the "Triad" - and the importance of post-transcriptional regulation of gene expression in the light of the recent finding that 90% of genomic DNA seems to be transcribed. Some previous attempts to provide a conceptual framework for these observations will be recalled, in particular the "Cascade Regulation Hypothesis" (CRH) developed in 1967-85, and the "Gene and Genon" concept proposed in 2007. A knowledge of the size of primary transcripts is of prime importance, both for experimental and theoretical reasons, since these molecules represent the primary units of the "RNA genome" on which most of the post-transcriptional regulation of gene expression occurs. In chapter 4, I will first discuss some current post-genomic topics before summarising the discovery of the high Mr-RNA transcripts, and the investigation of their processing spanning the last 50 years. Since even today, a consensus concerning the real form of primary transcripts in eukaryotic cells has not yet been reached, I will refer to the viral and specialized cellular models which helped early on to understand the mechanisms of RNA processing and differential splicing which operate in cells and tissues. As a well-studied example of expression and regulation of a specific cellular gene in relation to differentiation and pathology, I will discuss the early and recent work on expression of the globin genes in nucleated avian erythroblasts. An important concept is that the primary transcript not only embodies protein-coding information and regulation of its expression, but also the 3D-structure of the genomic DNA from which it was derived. The wealth of recent post-genomic data published in this field emphasises the importance of a fundamental principle of genome organisation and expression that has been overlooked for years even though it was already discussed in the 1970-80ties. These issues are addressed in chapter 5 which focuses on the involvement of the nuclear matrix and nuclear architecture in DNA and RNA biology. This section will make reference to the Unified Matrix Hypothesis (UMH), which was the first molecular model of the 3D organisation of DNA and RNA. The chapter on the "RNA-genome and peripheral memories" discusses experimental data on the ribonucleoprotein complexes containing pre-mRNA (pre-mRNPs) and mRNA (mRNPs) which are organised in nuclear and cytoplasmic spaces respectively. Finally, "Outlook " will enumerate currently unresolved questions in the field, and will propose some ideas that may encourage further investigation, and comprehension of available experimental data still in need of interpretation. In chapter 8, some propositions and paradigms basic to the authors own analysis are discussed. "In conclusion" the raison d'être of this review is recalled and positioned within the overall framework of scientific endeavour.

YTH-RNA-binding protein prevents deleterious expression of meiotic proteins by tethering their mRNAs to nuclear foci

Accurate and extensive regulation of meiotic gene expression is crucial to distinguish germ cells from somatic cells. In the fission yeast Schizosaccharomyces pombe, a YTH family RNA-binding protein, Mmi1, directs the nuclear exosome-mediated elimination of meiotic transcripts during vegetative proliferation. Mmi1 also induces the formation of facultative heterochromatin at a subset of its target genes. Here, we show that Mmi1 prevents the mistimed expression of meiotic proteins by tethering their mRNAs to the nuclear foci. Mmi1 interacts with itself with the assistance of a homolog of Enhancer of Rudimentary, Erh1. Mmi1 self-interaction is required for foci formation, target transcript elimination, their nuclear retention, and protein expression inhibition. We propose that nuclear foci formed by Mmi1 are not only the site of RNA degradation, but also of sequestration of meiotic transcripts from the translation machinery.

Paternal exposure to environmental 17-alpha-ethinylestradiol concentrations modifies testicular transcription, affecting the sperm transcript content and the offspring performance in zebrafish

The synthetic estrogen 17-α-ethinylestradiol (EE2), a major constituent in contraceptive pills, is an endocrine disrupting chemical (EDC) present in the aquatic environment at concentrations of ng/L. Developmental exposure to these low concentrations in fish can induce several disorders. Zebrafish (Danio rerio) is a perfect organism for monitoring the effects of environmental contaminants. Our hypothesis is that changes promoted by EE2 in the germ line of male adults could be transmitted to the unexposed progeny. We exposed male zebrafish to 2.5, 5 and 10ng/L of EE2 during spermatogenesis and mated them with untreated females. Detailed progeny development was studied concentrating to survival, hatching and malformations. Due to the high incidence of lymphedemas within larvae, we performed qPCR analysis of genes involved in lymphatic development (vegfc and vegfr3) and endothelial cell migration guidance (cxcr4a and cxcl12b). Estrogen receptor (ER) transcript presence was also evaluated in sperm, testis and embryos. Progenies showed a range of disorders although at a low incidence: skeletal distortions, uninflated swimbladder, lymphedema formation, cartilage deformities and otolith tethering. Swimming evaluation revealed less active locomotion. All these processes are related to pathways involving ERs (esr1, esr2a and esr2b). mRNA analysis revealed that environmental EE2 causes the up-regulation of esr1 an esr2b in testis and the increase of esr2b transcripts in sperm pointing to a link between lymphedema in embryos and ER expression impairment. We demonstrate that the effects induced by environmental toxicants can be paternally inherited and point to the changes on the sperm transcriptome as the responsible mechanism.