Developmental changes in RNA polymerase I and TATA box-binding protein during early Xenopus embryogenesis

Control of zygotic genome activation in Xenopus

The fertilized frog egg contains all the materials needed to initiate development of a new organism, including stored RNAs and proteins deposited during oogenesis, thus the earliest stages of development do not require transcription. The onset of transcription from the zygotic genome marks the first genetic switch activating the gene regulatory network that programs embryonic development. Zygotic genome activation occurs after an initial phase of transcriptional quiescence that continues until the midblastula stage, a period called the midblastula transition, which was first identified in Xenopus. Activation of transcription is programmed by maternally supplied factors and is regulated at multiple levels. A similar switch exists in most animals and is of great interest both to developmental biologists and to those interested in understanding nuclear reprogramming. Here we review in detail our knowledge on this major switch in transcription in Xenopus and place recent discoveries in the context of a decades old problem.

Global gene expression during early differentiation of Xenopus (Silurana) tropicalis gonad tissues

African clawed frog Xenopus sp. is used extensively for developmental biology and toxicology research. Amid concerns of environmental pollutants disrupting endocrine systems and causing altered reproductive development in wildlife, eco-toxicology research has led to a focus on linking molecular initiating events to population-level effects. As such, efforts to better understand reproductive development at the molecular level in these model species are warranted. To that end, transcriptomes were characterized in differentiating Xenopus tropicalis gonad tissues at Nieuwkoop and Faber (NF) stage 58 (pro-metamorphosis), NF66 (completion of metamorphosis), 1week post-metamorphosis (1WPM), and 2weeks post-metamorphosis (2WPM). Differential expression analysis between tissue types at each developmental stage revealed a substantial divergence of ovary and testis transcriptomes starting between NF58 and NF66; transcriptomes continued to diverge through 2WPM. Generally, testis-enriched transcripts were expressed at relatively constant levels, while ovary-enriched transcripts were up-regulated within this developmental period. Functional analyses of differentially expressed transcripts allowed linkages to be made between their putative human orthologues and specific cellular processes associated with differentiating gonad tissues. In ovary tissue, genetic programs direct germ cells through meiosis to the diplotene stage when maternal mRNAs are transcribed and trafficked to oocytes for translation following fertilization. In the testis, gene expression is consistent with connective tissue development, tubule formation, and germ cell support (Leydig and Sertoli cells). This dataset exhibited remarkable consistency with transcript profiles previously described in gonad tissues across species, and emphasizes the universal importance of certain transcripts for germ cell development and preparation of these tissues for reproduction.

Nucleolar development and allocation of key nucleolar proteins require de novo transcription in bovine embryos

The goal of the present study was to investigate whether key nucleolar proteins involved in ribosomal RNA (rRNA) transcription and processing are transcribed de novo or from maternally inherited messenger RNAs (mRNA) in bovine embryos, and to which extent de novo transcription of these proteins mRNA is required for the development of functional nucleoli during the major activation of the embryonic genome. Immunofluorescence for localization of key nucleolar proteins, autoradiography for detection of transcriptional activity, and transmission electron microscopy were applied to in vitro produced bovine embryos cultured from the 2-cell stage with or without (control groups) alpha-amanitin, which blocks the RNA polymerases II and III transcription and, thus the synthesis of mRNA. In the control groups, weak autoradiographic labeling was initially observed in the periphery of few nuclei at the 4-cell and the early 8-cell stage, and the entire nucleoplasm as well as nucleolus precursor bodies (NBBs) were prominently labelled in all late 8-cell stages. The NPBs displayed initial transformation into fibrillo-granular nucleoli. In the alpha-amanitin group, lack of autoradiographic labeling was seen at all developmental stages and disintegrated NPBs stage were found at the late 8-cell. Our immunofluorescence data indicate that RNA polymerase I, UBF, topoisomerase I and fibrillarin are transcribed de novo whereas nucleolin and nucleophosmin are maternally inherited as demonstrated by alpha -amanitin inhibition. However, localization of these two proteins to the nucleolar compartments was negatively affected by the alpha-amanitin treatment. Consequently, functional nucleoli were not established.

Nuclear reprogramming: the zygotic transcription program is established through an “erase-and-rebuild” strategy

Oocytes display a maternal-specific gene expression profile, which is switched to a zygotic profile when a haploid set of chromatin is passed on to the fertilized egg that develops into an embryo. The mechanism underlying this transcription reprogramming is currently unknown. Here we demonstrate that by the time when transcription is shut down in germinal vesicle oocytes, a range of general transcription factors and transcriptional regulators are dissociated from the chromatin. The global dissociation of chromatin factors (CFs) disrupts physical contacts between the chromatin and CFs and leads to erasure of the maternal transcription program at the functional level. Critical transcription factors and regulators remain separated from chromatin for a prolonged period, and become re-associated with chromatin shortly after pronuclear formation. This is followed temporally by the re-establishment of nuclear functions such as DNA replication and transcription. We propose that the maternal transcription program is erased during oogenesis to generate a relatively naïve chromatin and the zygotic transcription program is rebuilt de novo after fertilization. This process is termed as the "erase-and-rebuild" process, which is used to reset the transcription program, and most likely other nuclear processes as well, from a maternal one to that of the embryo. We further show in the accompanying paper (Gao T, et al., Cell Res 2007; 17: 135-150.) that the same strategy is also employed to reprogram transcriptional profiles in somatic cell nuclear transfer and parthenogenesis, suggesting that this model is universally applicable to all forms of transcriptional reprogramming during early embryogenesis. Displacement of CFs from chromatin also offers an explanation for the phenomenon of transcription silence during the maternal to zygotic transition.

Developmental and cell type-specific regulation of core promoter transcription factors in germ cells of frogs and mice

This article reports on the comparative cell type-specific expression profiles of selected core promoter-associated transcription factors during gametogenesis and embryogenesis in frogs and mice. In frogs we tested TBP, TRF2/TLF, TRF3, TFIIAalphabeta, and ALF, as well as variant forms of TAFs 4, 5, and 6. Four of these factors, TRF3, TAF4L, TAF5L, and the previously-characterized ALF gene, are preferentially expressed in testis and ovary. In mice we tested TBP, TRF2/TLF, TRF3, TFIIAalphabeta, and ALF. The results showed that while ALF was present in testis and ovary, as expected, TRF3 could only be detected in the ovary. RT-PCR experiments using RNAs from microdissected ovary tissue, together with in situ hybridization analysis, showed that TRF3 and ALF genes are specifically expressed in oocytes in both adult and prepubertal animals, whereas, their somatic counterparts, TBP and TFIIAalphabeta, are present in oocytes and in surrounding somatic cells of the follicle. Furthermore, both mice and frogs displayed a reduction in TRF3 and ALF transcript levels around the time of fertilization. In mice, transcripts from these genes could again be detected at low levels in embryonic reproductive tissues, but only reached maximal levels in adult animals. Finally, the results of protein-DNA interaction assays show that all combinations of core promoter complexes can be formed in vitro using recombinant TBP, TRF3, TFIIA, and ALF, including a TRF3-ALF complex. Overall, the diverse gene regulatory patterns observed here and in earlier reports indicate precise control over which transcription factor complexes can be formed in vivo during gametogenesis and early embryogenesis.

Basic mechanisms for the control of germ cell gene expression

The patterns of gene expression in spermatocytes and oocytes are quite different from those in somatic cells. The messenger RNAs produced by these cells are not only required to support germ cell development but, in the case of oocytes, they are also used for maturation, fertilization, and early embryogenesis. Recent studies have begun to provide an explanation for how germ-cell-specific programs of gene expression are generated. Part of the answer comes from the observation that germ cells express core promoter-associated regulatory factors that are different from those expressed in somatic cells. These factors supplement or replace their somatic counterparts to direct expression during meiosis and gametogenesis. In addition, germ cell transcription involves the recognition and use of specialized core promoter sequences. Finally, transcription must occur on chromosomal DNA templates that are reorganized into new chromatin-packaging configurations using alternate histone subunits. This article will review recent advances in our understanding of the factors and mechanisms that control transcription in ovary and testis and will discuss models for germ cell gene expression.

Cell and Molecular Biology of Nucleolar Assembly and Disassembly

Nucleoli disassemble in prophase of the metazoan mitotic cycle, and they begin their reassembly (nucleologenesis) in late anaphase?early telophase. Nucleolar disassembly and reassembly were obvious to the early cytologists of the eighteenth and nineteenth centuries, and although this has lead to a plethora of literature describing these events, our understanding of the molecular mechanisms regulating nucleolar assembly and disassembly has expanded immensely just within the last 10-15 years. We briefly survey the findings of nineteenth-century cytologists on nucleolar assembly and disassembly, followed by the work of Heitz and McClintock on nucleolar organizers. A primer review of nucleolar structure and functions precedes detailed descriptions of modern molecular and microscopic studies of nucleolar assembly and disassembly. Nucleologenesis is concurrent with the reinitiation of rDNA transcription in telophase. The perichromosomal sheath, prenucleolar bodies, and nucleolar-derived foci serve as repositories for nucleolar processing components used in the previous interphase. Disassembly of the perichromosomal sheath along with the dynamic movements and compositional changes of the prenucleolar bodies and nucleolus-derived foci coincide with reactivation of rDNA synthesis within the chromosomal nucleolar organizers during telophase. Nucleologenesis is considered in various model organisms to provide breadth to our understanding. Nucleolar disassembly occurs at the onset of mitosis primarily as a result of the mitosis-specific phosphorylation of Pol I transcription factors and processing components. Although we have learned much regarding nucleolar assembly and disassembly, many questions still remain, and these questions are as vibrant for us today as early questions were for nineteenth- and early twentieth-century cytologists.

Expression of the germ cell-specific transcription factor ALF in Xenopus oocytes compensates for translational inactivation of the somatic factor TFIIA

The discovery of germ cell-specific general transcription factor and coactivator variants has suggested that reproductive tissues control gene expression somewhat differently than somatic tissues. One of these factors, ALF (TFIIAtau), was first described as a testis-specific counterpart of the large (alpha/beta) subunit of TFIIA. Here we characterize endogenous ALF and TFIIA activities in the African clawed frog Xenopus laevis. ALF is present in both testis and ovary in this organism, and it completely replaces TFIIA in immature oocytes. When oocytes undergo progesterone-induced maturation, ALF activity disappears, and TFIIA activity is restored. Reactivation occurs through the translational up-regulation of two maternal TFIIAalpha/beta mRNAs and involves polyadenylation of a conserved 3'-untranslated region module. The effects of ALF overexpression and ALF immunodepletion on a thymidine kinase promoter construct demonstrate that this factor serves as an active replacement for TFIIA. In contrast, overexpression of TFIIA inhibits transcription, indicating that the somatic factor fails to function properly in the context of the oocyte transcription machinery. Overall, the results show that the translationally regulated reciprocal expression of ALF and TFIIA allows for the production of an active TFIIA-like general transcription factor throughout oogenesis.

Emerging concepts of nucleolar assembly

The nucleolus is a large nuclear domain and the site of ribosome biogenesis. It is also at the parting of the ways of several cellular processes, including cell cycle progression, gene silencing, and ribonucleoprotein complex formation. Consequently, a functional nucleolus is crucial for cell survival. Recent investigations of nucleolar assembly during the cell cycle and during embryogenesis have provided an integrated view of the dynamics of this process. Moreover, they have generated new ideas about cell cycle control of nucleolar assembly, the dynamics of the delivery of the RNA processing machinery, the formation of prenucleolar bodies, the role of precursor ribosomal RNAs in stabilizing the nucleolar machinery and the fact that nucleolar assembly is completed by cooperative interactions between chromosome territories. This has opened a new area of research into the dynamics of nuclear organization and the integration of nuclear functions.

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.

Ectopic expression of TATA box-binding protein induces shoot proliferation in Arabidopsis

The TATA box-binding protein (TBP) is an essential component of transcription initiation complexes of all three eukaryotic RNA polymerases. Increasing evidence suggests that the TBP activity and availability may be regulated to precisely control gene transcription and play an important role in cell type-specific regulation. Arabidopsis TBP-2 is up-regulated in apical shoot tissues. Overexpression of TBP-2 in transgenic Arabidopsis induces apical shoot proliferation. The expression of some shoot meristem regulatory genes is altered. These data suggest that the TBP gene dosage and/or expression level may play an important role in controlling shoot production and plant morphology.

Distinct roles for TBP and TBP-like factor in early embryonic gene transcription in Xenopus

The TATA-binding protein (TBP) is believed to function as a key component of the general transcription machinery. We tested the role of TBP during the onset of embryonic transcription by antisense oligonucleotide-mediated turnover of maternal TBP messenger RNA. Embryos without detectable TBP initiated gastrulation but died before completing gastrulation. The expression of many genes transcribed by RNA polymerase II and III was reduced; however, some genes were transcribed with an efficiency identical to that of TBP-containing embryos. Using a similar antisense strategy, we found that the TBP-like factor TLF/TRF2 is essential for development past the mid-blastula stage. Because TBP and a TLF factor play complementary roles in embryonic development, our results indicate that although similar mechanistic roles exist in common, TBP and TLF function differentially to control transcription of specific genes.

The ribosomal RNA processing machinery is recruited to the nucleolar domain before RNA polymerase I during Xenopus laevis development

Transcription and splicing of messenger RNAs are temporally and spatially coordinated through the recruitment by RNA polymerase II of processing factors. We questioned whether RNA polymerase I plays a role in the recruitment of the ribosomal RNA (rRNA) processing machinery. During Xenopus laevis embryogenesis, recruitment of the rRNA processing machinery to the nucleolar domain occurs in two steps: two types of precursor structures called prenucleolar bodies (PNBs) form independently throughout the nucleoplasm; and components of PNBs I (fibrillarin, nucleolin, and the U3 and U8 small nucleolar RNAs) fuse to the nucleolar domain before components of PNBs II (B23/NO38). This fusion process is independent of RNA polymerase I activity, as shown by actinomycin D treatment of embryos and by the lack of detectable RNA polymerase I at ribosomal gene loci during fusion. Instead, this process is concomitant with the targeting of maternally derived pre-rRNAs to the nucleolar domain. Absence of fusion was correlated with absence of these pre-rRNAs in nuclei where RNA polymerase II and III are inhibited. Therefore, during X. laevis embryogenesis, the recruitment of the rRNA processing machinery to the nucleolar domain could be dependent on the presence of pre-rRNAs, but is independent of either zygotic RNA polymerase I transcription or the presence of RNA polymerase I itself.

Translation of maternal TATA-binding protein mRNA potentiates basal but not activated transcription in Xenopus embryos at the midblastula transition

Early embryonic development in Xenopus laevis is characterized by transcriptional repression which is relieved at the midblastula stage (MBT). Here we show that the relative abundance of TATA-binding protein (TBP) increases robustly at the MBT and that the mechanism underlying this increase is translation of maternally stored TBP RNA. We show that TBP is rate-limiting in egg extract under conditions that titrate nucleosome assembly. Precocious translation of TBP mRNA in Xenopus embryos facilitates transcription before the MBT, without requiring TBP to be prebound to the promoter before injection. This effect is transient in the absence of chromatin titration and is sustained when chromatin is titrated. These data show that translational regulation of TBP RNA contributes to limitations on the transcriptional capacity before the MBT. Second, we examined the ability of trans-acting factors to contribute to promoter activity before the MBT. Deletion of cis-acting elements does not affect histone H2B transcription in egg extract, a finding indicative of limited trans-activation. Moreover, in the context of the intact promoter, neither the transcriptional activator Oct-1, nor TBP, nor TFIID enable transcriptional activation in vitro. HeLa cell extract, however, reconstitutes activated transcription in mixed extracts. These data suggest a deficiency in egg extract cofactors required for activated transcription. We show that the capacity for activated H2B transcription is gradually acquired at the early gastrula transition. This transition occurs well after the blastula stage when the basal transcription machinery can first be complemented with TBP.