Small nuclear RNA transcription and ribonucleoprotein assembly in early Xenopus development

A subset of yeast snRNA's contains functional binding sites for the highly conserved Sm antigen

Autoimmune sera of the Sm specificity react with the major class of small nuclear RNA (snRNA)-containing ribonucleoprotein particles (snRNP's) from organisms as evolutionarily divergent as insects and dinoflagellates but have been reported not to recognize snRNP's from yeast. The Sm antigen is thought to bind to a conserved snRNA motif that includes the sequence A(U3-6)G. The hypothesis was tested that yeast also contains functional analogues of Sm snRNA's, but that the Sm binding site in the RNA is more strictly conserved than the Sm antigenic determinant. After microinjection of labeled yeast snRNA's into Xenopus eggs or oocytes, two snRNA's from Saccharomyces cerevisiae become strongly immunoprecipitable with human auto-antibodies known as anti-Sm. These each contain the sequence A(U5-6)G, are essential for viability, and are constituents of the spliceosome. At least six other yeast snRNA's do not become immunoprecipitable and lack this sequence; these non-Sm snRNA's are all dispensable.

The two embryonic U1 RNA genes of Xenopus laevis have both common and gene-specific transcription signals

We have cloned and sequenced the 1842-bp repeat DNA encoding the two Xenopus laevis embryonic U1 RNAs, xU1a and xU1b. Although these two U1 RNAs are almost identical in sequence and are coordinately expressed during early embryogenesis, the flanking sequences of their genes show very little homology. Both genes contain two short conserved sequences, centered around positions -55 and +19, that probably are essential for 5' and 3' end formation of U1 RNAs, respectively. Efficient transcription of either gene in stage VI oocytes requires gene-specific promoter elements, located upstream of position -220. In the xU1b gene, these required 5'-flanking sequences include an 18-bp palindrome that has potential for Z-DNA formation. When injected separately into stage VI oocytes, the xU1a and xU1b genes are equally well transcribed, but co-injection of the two genes, either as the full length repeat or as two separate subclones, results in preferential accumulation of xU1b RNA. This competitive advantage of the xU1b gene in injected oocytes apparently is the result of preferred binding of one or more transcription factors that are limiting in these oocytes.

Repetitive sequence transcripts and U1 RNA in mouse oocytes and eggs

Others have reported that about two-thirds of the polyadenylated RNA of sea urchin or frog eggs contains short interspersed repetitive sequence transcripts, a much larger proportion than that found in mRNA of somatic cells. Thus, it appears that incompletely processed transcripts accumulate in these oocytes. Also, in what may be a related phenomenon, the nuclear concentration of U1 RNA (involved in processing hnRNA) decreases during growth of frog oocytes. To pursue this question in mammals, Northern blots of RNA from mouse oocytes and eggs collected before and after meiotic maturation were probed with genomic clones containing rodent Alu-equivalent sequences. The Alu sequence is the predominant short interspersed repetitive element in the genome and is abundant in hnRNA. When compared on the basis of mRNA content, the oocyte and egg RNA contained less short repetitive sequence transcripts than liver or brain cytoplasmic RNA. Using a U1 RNA-specific probe, the concentration of U1 RNA in mouse oocyte nuclei was found to be quite similar to that in somatic cells, and U1 RNA was stable during meiotic maturation. These results suggest that processing of transcripts in mouse oocytes does not possess the unusual features observed in lower animals.

The two embryonic U1 small nuclear RNAs of Xenopus laevis are encoded by a major family of tandemly repeated genes

We have identified a large family of U1 RNA genes in Xenopus laevis that encodes two distinct species of U1 RNA. These genes are expressed primarily at the onset of transcription in the 4,000-cell embryo (D. J. Forbes, M. W. Kirschner, D. Caput, J. E. Dahlberg, and E. Lund, Cell 38:681-689, 1984). The two types of embryonic U1 RNA genes are interspersed and are organized in large tandem arrays. The basic 1.9-kilobase repeating unit contains a single copy of each of the embryonic genes and is reiterated ca. 500-fold per haploid genome. This repetitive U1 DNA accounts for more than 90% of all U1 DNA in X. laevis. In addition to this major family, there exist several minor families of dispersed U1 RNA genes, which presumably encode the oocyte and somatic species of X. laevis U1 RNA. Although the embryonic genes are normally inactive in stage VI oocytes, they are expressed when cloned copies are injected into oocyte nuclei.

Autoradiographic studies on the distribution of labeled maternal RNA in early mouse embryos

Maternal RNA of mouse eggs and embryos was labeled by exposure of growing ovarian oocytes to 3H-uridine in vivo 8 to 16 days before ovulation and fertilization. Labeled embryos from the 1-cell stage to the blastocyst stage were collected, fixed, and autoradiographs of plastic sections prepared. The observed grain density was similar in the pronuclei and in the cytoplasm of 1-cell embryos. Knowing the volumes of nucleus and cytoplasm, it was determined that 3% of the maternal RNA was found in the pronuclei. It is suggested that some of this nuclear RNA may be stable small nuclear RNAs (e.g. U1 RNA) retained from the germinal vesicle stage through meiotic maturation. During the 2-cell stage and beyond, maternal RNA is degraded and labeled precursor is reincorporated into nuclear RNA, making it difficult to accurately quantitate the amount of nuclear maternal RNA. It is known that about one third of the total maternal RNA is lost between the 8-cell and blastocyst stages. It was found that cytoplasmic grain densities in inner and outer cells of the morula and blastocyst were not significantly different. Thus, the loss of maternal RNA does not proceed more rapidly in the differentiating trophoblast than in the inner cell mass.

Isolation and partial characterization of U1-U6 small RNAs from Bombyx mori

We have used a variety of techniques to characterize the U-series small nuclear RNAs from the posterior silk gland of Bombyx mori. Six molecular species have been identified which correspond to the vertebrate U1-U6 RNAs by the following criteria: (a) presence of the RNAs in ribonucleoprotein particles which can be immunoprecipitated by lupus Sm antisera; (b) presence of a 2,2,7-trimethylguanosine cap, as assayed by immunoprecipitation with anti-2,2,7-trimethylguanosine IgG; (c) size, as assayed by acrylamide/urea gel electrophoresis using HeLa cell U-RNA markers; and (d) primary nucleotide sequence, as determined by chemical/enzymatic cleavage of end-labeled molecules. The high conservation of primary sequence (66-81% homology based on partial sequences) relative to the corresponding vertebrate U-RNAs has permitted unambiguous identification of each molecule. With the exception of two subspecies of U3 RNA, the U-snRNAs of Bombyx exhibit a striking conservation of secondary structure relative to the proposed structures of the U-RNAs of vertebrates. This conservation is best exemplified by several compensatory base alterations that result in the maintenance of hairpin structures. These are particularly evident in U1 and U5 RNAs. Bombyx U3 is interesting in that two subspecies (of a total of four that were sequenced) diverge considerably in sequence (and presumably in structure) relative to the U3 RNA of vertebrates. The most abundant U-RNAs in the posterior silk gland appear to be U1 and U2, while U3-U6 are present in relatively small amounts.

Nuclear segregation of U2 snRNA requires binding of specific snRNP proteins

We analyzed the mechanism by which snRNAs are accumulated in the cell nucleus by introducing in vitro mutations into a cloned Xenopus U2 snRNA gene. The mutant genes were then expressed by microinjection into living oocytes. Using autoimmune antisera we localized the binding sites of snRNP proteins on the mutant U2 snRNAs. Sm antigen, a component shared by most U snRNPs, requires for binding a sequence containing AUUUUUG, a feature partly conserved in U1, U2, U4, and U5 snRNAs. A U2-specific protein defined by a second antiserum requires the two 3' loops of the U2 RNA molecule for binding. Mutant U2 transcripts unable to bind Sm antigen do not accumulate in the nucleus. Since Sm antigenic proteins are cytoplasmic and excluded from the oocyte nucleus when not bound to snRNA, we propose that a karyophilic domain may become exposed on formation of the RNA-protein complex.

The small nuclear RNAs of Drosophila

We have investigated the sequences of the major small nuclear RNAs of Drosophila cultured cells, with the objective of elucidating phylogenetically conserved primary and secondary structures by comparison of the data with previously determined sequences of these RNAs in vertebrate species. Our results reveal striking degrees of conservation between each Drosophila RNA and its vertebrate cognate, and also demonstrate blocks of homology among the Drosophila small nuclear RNAs, as previously described for vertebrates. The most conserved features include the 5' terminal region of U1 RNA, though to function in pre-mRNA splicing, most of the regions of U4 RNA recently implicated in 3' processing of pre-mRNA, and the major snRNP protein binding site ("domain A") that is also shared by vertebrate U1, U2, U4 and U5 RNAs. Several other conserved features have been revealed, suggesting additional regions of functional significance in these RNAs and also providing further insights into the evolutionary history of the small nuclear RNAs.

Ribonucleoprotein organization of eukaryotic RNA. XXXI. Structure of the U1 small nuclear ribonucleoprotein

A small nuclear ribonucleoprotein, U1 snRNP, has been implicated in mRNA processing. In this investigation sites of protein binding on U1 RNA were mapped by nuclease protection and RNA sequencing. Partially purified human U1 snRNP was sequentially digested with Escherichia coli RNAase III and S1 nuclease. The resistant ribonucleoprotein fragments were deproteinized, preparatively hybridized to the U1 RNA--complementary DNA strand of a human U1 gene cloned in bacteriophage M13, and displayed by electrophoresis. The nuclease-resistant U1 RNA fragments were between 23 and 63 nucleotides in length. Most of these fragments were not obtained when protein-free U1 RNA was similarly digested, whereas others were obtained in low yield from U1 RNA and much higher yield from U1 snRNP. RNA sequencing of the fragments revealed that the protein-protected sites in U1 snRNP correspond to base-paired stems I and II, loop a, and portions of stems III and IV (secondary structure nomenclature of Branlant et al., 1981). Single, "bulged" pyrimidines are present within the protein-covered helical regions of stems I and III. Most interestingly, the single-stranded 5' end of U1 RNA, implicated in mRNA splicing, was also highly protected by protein. These results demonstrate that the great majority of U1 RNA is covered by protein in U1 snRNP. The association of protein with the 5' end of U1 RNA is in agreement with recent evidence that snRNP proteins potentiate the binding of this region of U1 RNA with pre-mRNA splice sites.

The two embryonic U1 small nuclear RNAs of Xenopus laevis are encoded by a major family of tandemly repeated genes

We have identified a large family of U1 RNA genes in Xenopus laevis that encodes two distinct species of U1 RNA. These genes are expressed primarily at the onset of transcription in the 4,000-cell embryo (D. J. Forbes, M. W. Kirschner, D. Caput, J. E. Dahlberg, and E. Lund, Cell 38:681-689, 1984). The two types of embryonic U1 RNA genes are interspersed and are organized in large tandem arrays. The basic 1.9-kilobase repeating unit contains a single copy of each of the embryonic genes and is reiterated ca. 500-fold per haploid genome. This repetitive U1 DNA accounts for more than 90% of all U1 DNA in X. laevis. In addition to this major family, there exist several minor families of dispersed U1 RNA genes, which presumably encode the oocyte and somatic species of X. laevis U1 RNA. Although the embryonic genes are normally inactive in stage VI oocytes, they are expressed when cloned copies are injected into oocyte nuclei.

Differential expression of multiple U1 small nuclear RNAs in oocytes and embryos of Xenopus laevis

The small nuclear RNA, U1, is a highly conserved, 165 nucleotide long RNA which has been implicated in the processing of mRNA precursors. We present evidence that in the amphibian X. laevis there exist at least seven species of U1 RNA, which differ in sequence but not in length. Strikingly, these RNAs are not coordinately expressed. Two of the U1 RNAs are the predominant U1 species transcribed in the late blastula-early gastrula stages of Xenopus embryogenesis. These two RNAs, designated xU1a and xU1b, are not synthesized in significant amounts in stage 6 oocytes; a different set of U1 RNAs are expressed during late oogenesis. In a Xenopus cultured cell line, all of the U1 RNA species are expressed. Possible functions and developmental significance of these multiple U1 RNA species are discussed.

Small nuclear U-ribonucleoproteins in Xenopus laevis development. Uncoupled accumulation of the protein and RNA components

The accumulation of protein and RNA components of small nuclear U-ribonucleoprotein particles is non-co-ordinate during oogenesis and early embryogenesis in Xenopus laevis. Northern blot hybridization of a cloned Xenopus U2-RNA gene to oocyte and embryo RNAs demonstrates that the amount of small nuclear U2-RNA per oocyte reaches a plateau early in oogenesis (at the start of yolk deposition); further accumulation is not observed in oogenesis, nor in embryogenesis until the late blastula stage. In contrast, we show by immunoblot analysis that the proteins that bind to small nuclear U-RNAs continue to be accumulated after vitellogenesis begins, reaching maximum amounts only at the end of oocyte development. No further accumulation of these proteins is seen during embryogenesis. The consequences of this non-co-ordinate synthesis of small nuclear RNA and small nuclear RNA-binding proteins are as follows: a 10- to 20-fold excess of the protein components of the small ribonucleoprotein particles over small nuclear RNA exists in large oocytes; the bulk of the protein is cytoplasmic, while the RNA is nuclear. Thus the excess protein in the cytoplasm is uncomplexed with RNA. The imbalance between protein and RNA is not corrected until the late blastula or early gastrula stages of embryogenesis, when a tenfold increase in the amount of small nuclear U2-RNA is detected. Thus the protein, but not the RNA, components of small nuclear U-ribonucleoprotein particles are stockpiled in oocytes for later use in embryonic development. During the course of these studies, we also found that there are tissue-specific differences in the Sm-antigenic proteins of X. laevis.

Regulation of the cell cycle during early Xenopus development

Maturation-promoting factor (MPF) is a partially purified M-phase-specific activity that induces meiosis in frog oocytes and is detectable in mitotic lysates from cells of wide phylogenetic origins. We show here that without protein synthesis, addition and removal of MPF can drive the mitotic cycle in frog eggs, including nuclear membrane breakdown and reformation, chromosome condensation and decondensation, and suppression and initiation of DNA replication on endogenous DNA and on injected plasmid templates. We have also studied M-phase arrest induced by injection of unfertilized egg cytoplasm and show that this arrest blocks an endogenous cytoplasmic cell-cycle oscillator and causes the stabilization of MPF activity. The oscillator can be restarted by injection of Ca++, which causes chromosome decondensation, reinitiation of DNA replication, and loss of MPF activity. We have looked in more detail at how DNA replication responds to the level of MPF and show that the effects are on the chromatin template and not the replication machinery. These results suggest that in Xenopus embryos cell-cycle events of the nucleus, including DNA replication and mitosis, are controlled by the level of MPF activity, which is driven by or may be part of an autonomous cell-cycle oscillator. The way in which a more complicated somatic cell cycle may arise from the simple embryonic cell cycle is discussed.

Xenopus laevis U1 snRNA genes: characterisation of transcriptionally active genes reveals major and minor repeated gene families

Xenopus laevis U1 snRNA genes are found in several different genomic arrangements. The major family of genes is organised in tandem repeats of 1.8 kb. The minor U1-family is much less abundant and is present on 1.2-kb HinfI restriction fragments. In addition there are genomic arrangements present in one or very few copies, which could represent the ends of repeating units. There is no evidence for the presence of U1 pseudogenes in Xenopus. A cluster of U1 snRNA genes consisting of a member of the minor class of U1 snRNA genes and two of the 'rarely represented' genes was cloned. All three genes were expressed upon microinjection into frog oocytes. A fragment containing 149 bp of 5' flanking sequence, the RNA coding sequence, and 27 bp of 3' flanking sequence was shown to be accurately transcribed into U1 snRNA. These oocyte transcripts are assembled into specific U1 snRNPs. Sequence comparison of the regions flanking Xenopus U1 and U2 snRNA genes showed the presence of two blocks of homology, which are also conserved in many other U snRNA genes. One of these blocks is found at position -60 to -50 before the coding sequence, and we discuss its possible role in the correct initiation of transcription. The other is 3' to the coding sequence and may be involved in the accurate production of mature 3' ends in the RNA.

Drosophila melanogaster U1 and U2 small nuclear RNA genes contain common flanking sequences

The flanking sequences of three U2 genes (or pseudogenes) and one U1 gene of Drosophila melanogaster have been determined. Comparison of the sequences reveals a remarkable homology between position -30 and -65 upstream from the structural genes, starting with a TATA box-like sequence. The 3' flanking regions are also conserved in all genes and contain a canonical A-A-T-A-A-A polyadenylation signal.

Spontaneous formation of nucleus-like structures around bacteriophage DNA microinjected into Xenopus eggs

We have found that injection of bacteriophage lambda DNA into unfertilized Xenopus eggs causes the assembly around the DNA of structures resembling typical eucaryotic cell nuclei. These spherical structures begin to form 60-90 min after injection. They contain lambda DNA and are bounded by a phase-dense envelope. Immunofluorescent staining of the lambda-DNA-containing structures with anti-lamin antibody reveals the presence of the lamin nuclear proteins at the periphery of the structure, a pattern identical to that of embryonic nuclei. Electron microscopy reveals that the injected DNA is surrounded by a double bilayer nuclear membrane containing nuclear pore complexes. The "nuclei" containing lambda DNA respond to modulators of the Xenopus cell cycle in a manner that mimics the response of embryonic nuclei to these modulators during mitosis. These results suggest that nuclear reassembly and breakdown occur independently of specific DNA sequence information.

Maturation-promoting factor induces nuclear envelope breakdown in cycloheximide-arrested embryos of Xenopus laevis

We have studied the effect of maturation-promoting factor (MPF) on embryonic nuclei during the early cleavage stage of Xenopus laevis development. When protein synthesis is inhibited by cycloheximide during this stage, the embryonic cell cycle arrests in an artificially produced G2 phase-like state, after completion of one additional round of DNA synthesis. Approximately 100 nuclei can be arrested in a common cytoplasm if cytokinesis is first inhibited by cytochalasin B. Within 5 min after injection of MPF into such embryos, the nuclear envelope surrounding each nucleus disperses, as determined histologically or by immunofluorescent staining of the nuclear lamina with antilamin antiserum. The breakdown of the nuclear envelope occurs at levels of MPF comparable to or slightly lower than those required for oocyte maturation. Amplification of MPF activity, however, does not occur in the arrested egg as it does in the oocyte. These results suggest that MPF can act to advance interphase nuclei into the first events of mitosis and show that the nuclear lamina responds rapidly to MPF.