The role of cap methylation in the translational activation of stored maternal histone mRNA in sea urchin embryos

So close, no matter how far: multiple paths connecting transcription to mRNA translation in eukaryotes

Transcription of DNA into mRNA and translation of mRNA into proteins are two major processes underlying gene expression. Due to the distinct molecular mechanisms, timings, and locales of action, these processes are mainly considered to be independent. During the last two decades, however, multiple factors and elements were shown to coordinate transcription and translation, suggesting an intricate level of synchronization. This review discusses the molecular mechanisms that impact both processes in eukaryotic cells of different origins. The emerging global picture suggests evolutionarily conserved regulation and coordination between transcription and mRNA translation, indicating the importance of this phenomenon for the fine-tuning of gene expression and the adjustment to constantly changing conditions.

DHX15 regulates CMTR1-dependent gene expression and cell proliferation

DHX15 helicase regulates CMTR1-dependent first transcribed nucleotide ribose O-2 methylation.

CMTR1 contributes to mRNA cap formation by methylating the first transcribed nucleotide ribose at the O-2 position. mRNA cap O-2 methylation has roles in mRNA stabilisation and translation, and self-RNA tolerance in innate immunity. We report that CMTR1 is recruited to serine-5–phosphorylated RNA Pol II C-terminal domain, early in transcription. We isolated CMTR1 in a complex with DHX15, an RNA helicase functioning in splicing and ribosome biogenesis, and characterised it as a regulator of CMTR1. When DHX15 is bound, CMTR1 activity is repressed and the methyltransferase does not bind to RNA pol II. Conversely, CMTR1 activates DHX15 helicase activity, which is likely to impact several nuclear functions. In HCC1806 breast carcinoma cell line, the DHX15–CMTR1 interaction controls ribosome loading of a subset of mRNAs and regulates cell proliferation. The impact of the CMTR1–DHX15 interaction is complex and will depend on the relative expression of these enzymes and their interactors, and the cellular dependency on different RNA processing pathways.

Regulation and function of CMTR1-dependent mRNA cap methylation

mRNA is modified co-transcriptionally at the 5' end by the addition of an inverted guanosine cap structure which can be methylated at several positions. The mRNA cap recruits proteins involved in gene expression and identifies the transcript as being cellular or 'self' in the innate immune response. Methylation of the first transcribed nucleotide on the ribose 2'-O position is a prevalent cap modification which has roles in splicing, translation and provides protection against the innate immune response. In this review, we discuss the regulation and function of CMTR1, the first transcribed nucleotide ribose 2'-O methyltransferase, and the molecular interactions which mediate methylated 2'-O ribose function. WIREs RNA 2017, 8:e1450. doi: 10.1002/wrna.1450 For further resources related to this article, please visit the WIREs website.

Oocyte quality and maternal control of development

The oocyte is a unique and highly specialized cell responsible for creating, activating, and controlling the embryonic genome, as well as supporting basic processes such as cellular homeostasis, metabolism, and cell cycle progression in the early embryo. During oogenesis, the oocyte accumulates a myriad of factors to execute these processes. Oogenesis is critically dependent upon correct oocyte-follicle cell interactions. Disruptions in oogenesis through environmental factors and changes in maternal health and physiology can compromise oocyte quality, leading to arrested development, reduced fertility, and epigenetic defects that affect long-term health of the offspring. Our expanding understanding of the molecular determinants of oocyte quality and how these determinants can be disrupted has revealed exciting new insights into the role of oocyte functions in development and evolution.

Incomplete RNA polymerase II phosphorylation in Xenopus laevis early embryos

Phosphorylation of RNA polymerase II largest subunit on its C-terminal domain (CTD) heptapeptide repeats has been shown to play a key role in the regulation of mRNA synthesis and processing. In many higher metazoans, early embryos do not synthesise mRNAs during the first cell cycles following fertilisation. Transcription resumes and becomes an absolute requirement for development after several cell cycles characteristic of each species. Therefore, CTD phosphorylation has been investigated during early development of the African clawed-frog Xenopus laevis. Fertilisation is shown to trigger an abrupt dephosphorylation of the CTD. Phosphorylation of the CTD resumes concurrently with the mid-blastula transition (MBT). Both are advanced with polyspermy and increased temperatures; they do not occur when replication is impaired with aphidicolin. In Xenopus laevis somatic cells, a set of monoclonal antibodies defined distinct phosphoepitopes on the CTD. Two of them were absent before the MBT indicating that the CTD lacks the phosphorylation at the serine-2 position of the heptapeptide. The possible contribution of RNA polymerase II phosphorylation to the developmental-regulation of maternal mRNA processing in embryos is discussed.

Control of translation initiation in animals

Regulation of translation initiation is a central control point in animal cells. We review our current understanding of the mechanisms of regulation, drawing particularly on examples in which the biological consequences of the regulation are clear. Specific mRNAs can be controlled via sequences in their 5' and 3' untranslated regions (UTRs) and by alterations in the translation machinery. The 5'UTR sequence can determine which initiation pathway is used to bring the ribosome to the initiation codon, how efficiently initiation occurs, and which initiation site is selected. 5'UTR-mediated control can also be accomplished via sequence-specific mRNA-binding proteins. Sequences in the 3' untranslated region and the poly(A) tail can have dramatic effects on initiation frequency, with particularly profound effects in oogenesis and early development. The mechanism by which 3'UTRs and poly(A) regulate initiation may involve contacts between proteins bound to these regions and the basal translation apparatus. mRNA localization signals in the 3'UTR can also dramatically influence translational activation and repression. Modulations of the initiation machinery, including phosphorylation of initiation factors and their regulated association with other proteins, can regulate both specific mRNAs and overall translation rates and thereby affect cell growth and phenotype.

Modifications of the 5' cap of mRNAs during Xenopus oocyte maturation: independence from changes in poly(A) length and impact on translation

The translation of specific maternal mRNAs is regulated during early development. For some mRNAs, an increase in translational activity is correlated with cytoplasmic extension of their poly(A) tails; for others, translational inactivation is correlated with removal of their poly(A) tails. Recent results in several systems suggest that events at the 3' end of the mRNA can affect the state of the 5' cap structure, m7G(5')ppp(5')G. We focus here on the potential role of cap modifications on translation during early development and on the question of whether any such modifications are dependent on cytoplasmic poly(A) addition or removal. To do so, we injected synthetic RNAs into Xenopus oocytes and examined their cap structures and translational activities during meiotic maturation. We draw four main conclusions. First, the activity of a cytoplasmic guanine-7-methyltransferase increases during oocyte maturation and stimulates translation of an injected mRNA bearing a nonmethylated GpppG cap. The importance of the cap for translation in oocytes is corroborated by the sensitivity of protein synthesis to cap analogs and by the inefficient translation of mRNAs bearing nonphysiologically capped 5' termini. Second, deadenylation during oocyte maturation does not cause decapping, in contrast to deadenylation-triggered decapping in Saccharomyces cerevisiae. Third, the poly(A) tail and the N-7 methyl group of the cap stimulate translation synergistically during oocyte maturation. Fourth, cap ribose methylation of certain mRNAs is very inefficient and is not required for their translational recruitment by poly(A). These results demonstrate that polyadenylation can cause translational recruitment independent of ribose methylation. We propose that polyadenylation enhances translation through at least two mechanisms that are distinguished by their dependence on ribose modification.

Mechanisms of translational control in early development

Oocytes accumulate a dowry of maternal mRNAs in preparation for embryogenesis. These maternal transcripts are kept dormant until late oogenesis or early embryogenesis when their translation is activated. In recent years, three types of translational control acting on maternal mRNAs have emerged: translational activation by cytoplasmic polyadenylation, translational activation by RNA localization, and regulated translational repression. In each case, translational control depends on the binding of trans-acting factors to sequences in the 3' untranslated region (3'UTR). Identification of these trans-acting factors is beginning to shed light on the molecular mechanisms that mediate translational control.

Translational regulation of maternal mRNAs

Translational regulation of maternal mRNAs serves to constrain their activities in both time and space. Both types of constraint might be expected to be critical for normal development and the rather short list of maternal mRNAs for which this has been shown to be true has expanded considerably over the past year. Substantial progress has also been reported in the identification and characterization of the cis-acting elements and trans-acting factors that mediate translational regulation and their interactions with one another.

mRNA transport in yeast: time to reinvestigate the functions of the nucleolus

Nucleocytoplasmic transport of mRNA is vital to gene expression and may prove to be key to its regulation. Genetic approaches in Saccharomyces cerevisiae have led to the identification of conditional mutants defective in mRNA transport. Mutations in approximately two dozen genes result in accumulation of transcripts, trapped at various sites in the nucleus, as detected by in situ hybridization. Phenotypic and molecular analyses of many of these mRNA transport mutants suggest that, in yeast, the function of the nucleus is not limited to the biogenesis of pre-ribosomes but may also be important for transport of poly(A)+ RNA. A similar function of the animal cell nucleolus is suggested by several observations.

Transport of RNA between nucleus and cytoplasm

The transport out of the nucleus of RNAs transcribed by RNA polymerase II (U snRNAs and mRNAs) has not been extensively studied. Basic questions, such as whether export requires association of the RNA with specific proteins, are not yet definitively answered. Nevertheless, recent progress in this area has been significant. Sequence or structural features of RNAs which are either required for export or which result in nuclear retention have been defined. These are presumed to interact with components of the transport machinery or with anchoring nuclear factors respectively. The unexplained dependence of the transport of certain mRNAs on either intervening sequences or for transcription from specific promoters suggests that RNAs may have to pass through different intranuclear compartments before export. Studies of the import of RNAs from the cytoplasm has revealed that different classes of nuclear localization signals exist, and protein components of viral RNPs that appear to determine the direction in which they move through the nuclear envelope have been identified.

A conditional yeast mutant deficient in mRNA transport from nucleus to cytoplasm

Transport of mRNA from nucleus to cytoplasm is critical for eukaryotic gene expression; however, the mechanism of export is unknown. Selection and screening procedures have therefore been used to obtain a family of temperature-sensitive conditional mutants of Saccharomyces cerevisiae that accumulate poly(A)+ RNA in the nucleus when incubated at 37 degrees C, as judged by in situ hybridization. In one such mRNA transport mutant, mtr1-1, RNA synthesis continues, the export of poly(A)+ RNA is inhibited, intranuclear poly(A)+ is remarkably stable, and protein synthesis gradually stops. Thus, there is no tight coupling between RNA synthesis and export. The export lesion is reversible. Although mRNA export is clearly not a default option, neither inhibition of protein synthesis, inhibition of mRNA splicing, nor inhibition of poly(A)-binding protein function blocks export of the average poly(A)+, as judged by in situ hybridization. Further analysis of the family of mtr mutants should help map the path of RNA transport.

Sequence elements that affect mRNA translational activity in developing Dictyostelium cells

Post-transcriptional controls, including changes in both mRNA translational activity and stability, play an important role in the regulation of ribosomal protein gene expression in developing Dictyostelium discoideum cells. Previously we have shown that the mechanisms which regulate the translational activity of the r-protein mRNAs operate at the level of translational initiation and do not involve changes in polyadenylation or capping. By analysing the translational behavior of chimeric and mutant mRNAs in transformed cells, we have now been able to localize the determinants of translational activity of one of the r-protein mRNAs to the 5'-untranslated region. Although this and other r-protein mRNAs differ strikingly from the Dictyostelium consensus in the region of the initiator AUG codon, we find that improving the match to that consensus does not increase the translational activity of the message in developing cells. Current experiments are designed to determine whether translational regulation is mediated by strong interactions with specific inhibitors or by weak interactions with translational initiation factors.

DNA synthesis and the control of embryonic gene expression in C. elegans

DNA synthesis in each cell lineage of the early C. elegans embryo was measured using microspectrofluorimetry. Aphidicolin was shown to inhibit DNA synthesis almost instantly and completely. Aphidicolin was then used to investigate how DNA synthesis controls expression of two biochemical markers that appear at different times during gut development: gut granules and a carboxylesterase. We show that marker expression is controlled neither by reaching the normal DNA: cytoplasm ratio, by counting the normal number of rounds of DNA synthesis, nor by a simple lengthening of the cell cycle. Instead, expression of both gut markers requires a short period of DNA synthesis in the first cell cycle after the gut has been clonally established.

Cell cycles and in vitro transdifferentiation and regeneration of isolated, striated muscle of jellyfish

Isolated, mononucleated, cross-striated muscle cells of a medusa can transdifferentiate in vitro to various new cell types and even form a complex regenerate. The transdifferentiation events follow a strict pattern. The first new cell type resembles smooth muscle and is formed without a preceding DNA replication. This cell type behaves like a stem cell and by quantal cell cycles produces all other new cell types. Some preparations develop an inner and an outer layer separated by a basal lamella. Formation of these layers does not depend on DNA replication. When layers do not form, each division results in nerve cells and smooth muscle cells. If separation into layers occurs, then a regenerate will be formed, and in the course of only two cell cycles all necessary cell types to form a functional regenerate will differentiate.

Translation of mouse testis poly(A)+ mRNAs for testis-specific protein, protamine 1, and the precursor for protamine 2

Since previous studies have suggested that the mammalian protamine mRNAs are translated poorly in cell-free systems, we directly measured the efficiency of translation of mouse protamine 1 mRNA. We found that mouse testis poly(A)+ mRNA stimulates the synthesis in the wheat germ and reticulocyte cell-free systems of three prominant translation products which can be resolved by electrophoresis through acid urea polyacrylamide gels containing 8 M urea. These translation products have been identified as testis-specific protein, protamine 1, and the precursor to protamine 2 by several criteria, including labeling with amino acids, [35S]cysteine, and [3H]leucine, which are known to be specific to some of these proteins from the nucleotide sequences of recombinant DNAs. Surprisingly, the mobility of the testis-specific protein translation product is slightly reduced and the mobility of both protamine translation products is drastically reduced unless the extracts of cell-free translations are coelectrophoresed with the appropriate carrier. The fraction of [35S]cysteine- labeled protamine 1 translation product was compared with the fraction of testis poly(A)+ mRNA as protamine 1 mRNA which we measured in dot blots with the use of an SP6 RNA polymerase transcript for protamine 1. The results demonstrate that protamine 1 mRNA is translated only slightly less efficiently than the average testis poly(A)+ mRNA.

Three translationally regulated mRNAs are stored in the cytoplasm of clam oocytes

In situ hybridization was used to examine the spatial distributions of three translationally controlled maternal RNAs in oocytes and two-cell embryos of the clam Spisula. 3H-labeled single-stranded RNA probes were generated from SP6 recombinant clones containing DNA inserts encoding portions of histone H3 (the DNA sequence which is presented here), cyclin A, and the small subunit of ribonucleotide reductase. Hybridization of these probes to oocytes, in which the mRNAs are translationally inactive, shows that these mRNAs are stored in the cytoplasm. There is no evidence for sequestration of any of the RNAs within the nucleus or any other discrete structure. Instead they appear to be evenly distributed throughout the cytoplasm.

Inhibitor of eukaryotic initiation factor 4F activity in unfertilized sea urchin eggs

Extracts from unfertilized sea urchin eggs contain an inhibitor of translation that inhibits protein synthesis in cell-free translation systems from sea urchin embryos or rabbit reticulocytes. The inhibitory effects of egg extracts can be reversed by the addition of mammalian eukaryotic initiation factor 4F (eIF-4F) in both sea urchin embryo and reticulocyte systems, suggesting that the inhibitor inactivates this initiation factor. The accumulated data suggest that the ability of eIF-4F to recycle may be compromised. The addition of eIF-4F to cell-free translation systems from unfertilized sea urchin eggs also stimulates protein synthesis. However, the stimulation does not increase protein synthetic activity in the egg cell-free translation system to the levels observed in those produced from 2-hr embryos. This suggests that, although the unfertilized egg contains an inhibitor of eIF-4F and reduced levels of eIF-4F activity, inactivation of this component is only one of the factors involved in the low rate of maternal mRNA utilization found prior to fertilization.

Expression of epidermis-specific antigens during embryogenesis of the ascidian, Halocynthia roretzi

We have produced two monoclonal antibodies (Epi-1 and Epi-2) which specifically recognize epidermal cells and their derivative, the larval tunic, of developing embryos of the ascidian Halocynthia roretzi. The antigens, examined by indirect immunofluorescence staining, first appear at the early tailbud stage and are present until at least the swimming larval stage. There were distinct and separate puromycin and actinomycin D sensitivity periods for each antigen. Aphidicolin, a specific inhibitor of DNA synthesis, prevented the appearance of each antigen when embryos were exposed to the drug continuously from cleavage stages. These results suggest that the antigens are synthesized during embryogenesis by developing epidermal cells and that several rounds of DNA replication are required for the antigen expression. Early cleavage stage embryos, including fertilized but unsegmented eggs, in which cytokinesis had been blocked with cytochalasin B expressed the antigens, and blastomeres exhibiting the antigens were always of the epidermis lineage. In partial embryos produced by four separated blastomere pairs of the 8-cell embryos, the expression of antigens was seen only in those developed from the animal blastomere pairs, which are progenitors of epidermal cells. These observations indicate that differentiation of epidermal cells in ascidian embryos takes place in a typical "mosaic" fashion.

Translation of maternal histone mRNAs in sea urchin embryos: a test of control by 5' cap methylation

Recent results have demonstrated the occurrence of mRNA cap methylation in the sea urchin embryo following fertilization. It has been suggested that this methylation event is responsible for the translational activation of maternal histone mRNAs in these embryos. We have used aphidicolin, an effective inhibitor of both DNA synthesis and cap methylation in cleavage stage sea urchin embryos, to examine the relationship between cap methylation and translation. At 5 micrograms/ml, a dose which rapidly abolishes DNA replication and blocks cleavage, we note no effect on recruitment or translation of maternal alpha-subtype histone mRNAs. This suggests that a postfertilization cap methylation event is not critical to the process of regulation of the translation of stored alpha-subtype histone mRNAs.