Message sequences and short repetitive sequences are interspersed in sea urchin egg poly(A)+ RNAs

Generation of Drosophila sisRNAs by Independent Transcription from Cognate Introns

Although stable intronic sequence RNAs (sisRNAs) are conserved in plants and animals, their functional significance is still unclear. We identify a pool of polyadenylated maternally deposited sisRNAs in Drosophila melanogaster. These sisRNAs can be generated by independent transcription from the cognate introns. The ovary-specific poly(A) polymerase Wispy mediates the polyadenylation of maternal sisRNAs and confers their stability as maternal transcripts. A developmentally regulated sisRNA sisR-3 represses the expression of a long noncoding RNA CR44148 and is required during development. Our results expand the pool of sisRNAs and suggest that sisRNAs perform regulatory functions during development in Drosophila.

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Identification of polyadenylated sisRNAs

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sisRNAs can be produced from independent transcription

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sisR-3 regulates a long noncoding RNA

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sisR-3 is required during development

Poly(A) RNA of the egg cytoplasm: structural resemblance to the nuclear RNA of somatic cells

This paper concerns the structural characteristics of the poly(A) RNA stored in unfertilized amphibian and echinoderm eggs. Though located in the egg cytoplasm, at least two-thirds of these maternal transcripts display an interspersed sequence organization similar to that of nuclear RNA. In Xenopus laevis interspersed poly(A) RNA molecules are synthesized and deposited in the oocyte cytoplasm throughout the main growth phase of oogenesis. Regions of the sea urchin genome that are represented by interspersed maternal transcripts have been recovered from recombinant clone libraries. In one case the same single-copy sequence is found both in an abundant message-sized 1.6 kilobase (kb) maternal transcript and in a 7.5 kb maternal transcript that structurally resembles a precursor form and is not found in embryonic polysomes. In a second example considered, a 9.5 kb transcript was identified in embryo nuclear RNA that may be identical in structure with an interspersed maternal poly(A) RNA derived from the same transcription unit. Transcription of this sequence appears to be constitutive in somatic cell nuclei, though no homologous cytoplasmic RNAs are found after early cleavage. This may be a widespread form of regulation for transcription units expressed in female germ cells, and represented in the maternal poly(A) RNA pools of unfertilized eggs.

Coordinated and conserved expression of alphoid repeat and alphoid repeat-tagged coding sequences

We have found an alpha-like simple-sequence DNA repeat that is differentially expressed during early embryogenesis in both chick and zebrafish. Before and during the primitive streak stage, transcripts of the alphoid repeat sequence were ubiquitously expressed throughout zebrafish and chick embryos. After headfold formation, expression was limited to the cardiac neural crest, the head, and the heart. Two types of alphoid repeat sequence transcripts were identified: alphoid repeat RNA and alphoid repeat-tagged mRNA (ESalphaT). Several of the ESalphaTs were identified by (1) searching expressed sequence tag databases, (2) arbitrary rapid amplification of cDNA ends (RACE), and (3) screening embryonic cDNA libraries. The alphoid element was located in the 3' untranslated region of one ESalphaT that was obtained by RACE. The ESalphaT sequences encoded a variety of different types of proteins, but all were expressed within tissues that were positive for the alphoid repeat RNA. The presence of two types of coordinately expressed alphoid-like repeat transcripts in maternal RNA with subsequent restriction to the head and heart, and the conservation of these features in disparate vertebrate embryos, suggest that the alphoid repeat sequence may serve as a control element in the gene regulation network.

Patterns of gene expression in the developing adult sea urchin central nervous system reveal multiple domains and deep-seated neural pentamery

The adult sea urchin central nervous system (CNS) is composed of five radial nerve cords connected to a circular nerve ring. Although much is known about the molecular mechanisms underlying the development and function of the nervous systems of many invertebrate and vertebrate species, virtually nothing is known about these processes in echinoderms. We have isolated a set of clones from a size-selected cDNA library prepared from the nervous system of the sea urchin Heliocidaris erythrogramma for use as probes. A total of 117 expressed sequence clones were used to search the GenBank database. Identified messages include genes that encode signaling proteins, cytoskeletal elements, cell surface proteins and receptors, cell proliferation and differentiation factors, transport and channel proteins, and a RNA DEAD box helicase. Expression was analyzed by RNA gel blot hybridization to document expression through development. Many of the genes have apparently neural limited expression and function, but some have been co-opted into new roles, notably associated with exocytotic events at fertilization. Localization of gene expression by whole-mount in situ hybridization shows that the morphologically simple sea urchin radial CNS exhibits complex organization into localized transcriptional domains. The transcription patterns reflect the morphological pentamery of the echinoderm CNS and provide no indication of an underlying functional bilateral symmetry in the CNS.

A possible meiotic function of the peculiar patterns of gene expression in mammalian spermatogenic cells

This review focuses on the striking differences in the patterns of transcription and translation in somatic and spermatogenic cells in mammals. In early haploid cells, mRNA translation evidently functions to restrict the synthesis of certain proteins, notably protamines, to transcriptionally inert late haploid cells. However, this does not explain why a substantial proportion of virtually all mRNA species are sequestered in translationally inactive free-messenger ribonucleoprotein particles (free-mRNPs) in meiotic cells, since most mRNAs undergo little or no increase in translational activity in transcriptionally active early haploid cells. In addition, most mRNAs in meiotic cells appear to be overexpressed because they are never fully loaded on polysomes and the levels of the corresponding protein are often much lower than the mRNA and are sometimes undetectable. A large number of genes are expressed at grossly higher levels in meiotic and/or early haploid spermatogenic cells than in somatic cells, yet they too are translated inefficiently. Many genes utilize alternative promoters in somatic and spermatogenic cells. Some of the resulting spermatogenic cell-altered transcripts (SCATs) encode proteins with novel functions, while others contain features in their 5'-UTRs, secondary structure or upstream reading frames, that are predicted to inhibit translation. This review proposes that the transcriptional machinery is modified to provide access to specific DNA sequences during meiosis, which leads to mRNA overexpression and creates a need for translational fine-tuning to prevent deleterious consequences of overproducing proteins.

EST analysis of gene expression in early cleavage-stage sea urchin embryos

A set of 956 expressed sequence tags derived from 7-hour (mid-cleavage) sea urchin embryos was analyzed to assess biosynthetic functions and to illuminate the structure of the message population at this stage. About a quarter of the expressed sequence tags represented repetitive sequence transcripts typical of early embryos, or ribosomal and mitochondrial RNAs, while a majority of the remainder contained significant open reading frames. A total of 232 sequences, including 153 different proteins, produced significant matches when compared against GenBank. The majority of these identified sequences represented ‘housekeeping’ proteins, i.e., cytoskeletal proteins, metabolic enzymes, transporters and proteins involved in cell division. The most interesting finds were components of signaling systems and transcription factors not previously reported in early sea urchin embryos, including components of Notch and TGF signal transduction pathways. As expected from earlier kinetic analyses of the embryo mRNA populations, no very prevalent protein-coding species were encountered; the most highly represented such sequences were cDNAs encoding cyclins A and B. The frequency of occurrence of all sequences within the database was used to construct a sequence prevalence distribution. The result, confirming earlier mRNA population analyses, indicated that the poly(A) RNA of the early embryo consists mainly of a very complex set of low-copy-number transcripts.

Toward the gene catalogue of sea urchin development: the construction and analysis of an unfertilized egg cDNA library highly normalized by oligonucleotide fingerprinting

We describe the use of oligonucleotide fingerprinting for the generation of a normalized cDNA library from unfertilized sea urchin eggs and report the preliminary analysis of this library, which resulted in the establishment of a partial gene catalogue of the sea urchin egg. In an analysis of 21,925 cDNA clones by hybridization with 217 oligonucleotide probes, we were able to identify 6291 clusters corresponding to different transcripts, ranging in size from 1 to 265 clones. This corresponds to an average 3.5-fold normalization of the starting library. The normalized library represents about one-third of all genes expressed in the sea urchin egg. To generate sequence information for the transcripts represented by the clusters, representative clones selected from 711 clusters were sequenced. The construction and preliminary analysis of the normalized library are the first steps in the assembly of an increasingly complete collection of maternal genes expressed in the sea urchin egg, which will provide a number of insights into the early development of this well-characterized model organism.

Organization and expression of multiple actin genes in the sea urchin

A set of at least 11 actin genes has been isolated from genomic recombinant deoxyribonucleic acid libraries of the sea urchin Strongylocentrotus purpuratus. Most of the isolates derive from a library which represents the genome of a single animal. There are at least five distinct types of sea urchin actin gene, some of which are represented by multiple copies in the genome. The actin gene types are distinguished by nonhomologous flanking sequences and intervening sequences, though the protein coding sequences appear in most cases to be quite similar. Eight of the 11 genes isolated have been recovered in lambda recombinants that contain two actin genes, linked at 5- to 9-kilobase distances. Restriction map overlaps suggest that the genome contains an array of at least three of these genes spaced over about 30 kilobases of deoxyribonucleic acid. In the linkage patterns observed, actin genes of diverse types were linked to each other. In early embryos, actin messenger ribonucleic acid (RNA) transcripts of 1.8 and 2.2 kilobases were found, and the longer of these transcripts was more prevalent in the maternal RNA of the egg. From RNA gel blot experiments, we conclude that the two transcripts derive from different actin gene types. Different repetitive sequences were located to either side of most of the actin genes, and in most observed cases the repeat sequences which were adjacent to actin genes of a given type were similar. The repeat sequences flanking the actin genes belonged to families which were transcribed, but those repeats in the neighborhood of the actin genes which have been investigated were not themselves represented in the stable RNAs of eggs or early embryos.

Enrichment of middle repetitive element Bm-1 transcripts in translationally active RNA fractions of the silkmoth, Bombyx mori

The Bm-1 repetitive element family represents a group of transcribed repetitive sequences in the genome of the silkmoth Bombyx mori. In the Bm-5 and BmN permanent cell lines studied here, alpha-amanitin inhibition and nuclear 'run-on' experiments demonstrated that approximately 80% of the Bm-1 transcripts are produced by RNA polymerase II. Bm-1 transcripts are dramatically enriched in poly A+ and polysomal RNA fractions compared to total RNA in these two cell lines. In the Bm-5 cell line, from total to poly A+ and polysomal RNA fractions, Bm-1 transcripts are enriched approximately 4 and 2 times, respectively, while in the BmN cell line these same fractions are enriched about 2 and 19 times compared to total RNA. This suggests that the Bm-1 transcripts may be involved in post-transcriptional processes or control of translation. Our data also revealed less size heterogeneity of Bm-1 transcripts in polysomal as compared to nuclear fractions. In the Bm-5 and BmN cell lines, the size of most transcripts containing Bm-1 sequences increases from approximately 1700 nt in the nucleus to 3000 nt in the polysomal fraction, both fractions with RNA much larger than the Bm-1 consensus sequence (250 bp). This raises the possibility that some Bm-1 elements are transcribed as part of larger transcripts containing mRNA by way of 'read-through', and may be involved in post-transcriptional regulation of gene expression as cis and/or trans acting elements.

Xenopus interspersed RNA families, Ocr and XR, bind DNA-binding proteins

Interspersed RNA makes up two-thirds of cytoplasmic polyadenylated RNA in Xenopus and sea urchin eggs. Although it has no known function, previous work has suggested that at least one family of interspersed RNA, XR, binds Xenopus oocyte proteins, and can influence the rate of translation. We have used two Xenopus repeat families, Ocr and XR, to explore their protein binding abilities. Ocr RNA binds the same pattern of highly abundant oocyte proteins that XR RNA binds, which are believed to be messenger ribonucleoprotein (mRNP) particle proteins. In addition, we show that Ocr RNA binds the Oct-60 protein, a member of the POU-domain family of transcription factors found in Xenopus oocytes. Using a 32 base pair sequence from the XR repeat in a DNA affinity column two proteins were isolated, 66 kDa and 92 kDa, that together form a complex with XR DNA. One of these proteins (92 kDa) also binds XR RNA. We suggest that the role of at least a subset of interspersed RNAs in development may be to bind, and sequester in the cytoplasm, DNA-binding proteins until the end of oogenesis.

Evidence that XR family interspersed RNA may regulate translation in Xenopus oocytes

It has been shown that about two thirds of Xenopus oocyte or sea urchin egg cytoplasmic poly(A)+ RNA contains interspersed repetitive sequences. The functional significance of this interspersed RNA has remained unknown. Here the function of a subfamily of interspersed RNA (XR family; McGrew and Richter, 1989: Dev Biol 134:267-270) in Xenopus oocytes was studied. We found that the elimination of T7 XR (one of the two complementary strands of the XR repeat) interspersed RNA by complementary oligodeoxynucleotides significantly inhibited protein synthesis. On the other hand, the injection of in vitro synthesized T7 XR RNA stimulated translation. Moreover, the insertion of the T7 XR RNA sequence into globin mRNA repressed the translation of the globin mRNA. In order to explain these results, we analyzed interactions between the XR interspersed RNA and oocyte proteins. We found that the major XR RNA binding proteins were p56 and p60, which could be the known mRNA "masking" proteins that bind mRNA and inhibit translation. Further, a 42 kD protein has been identified that appears to bind T7 XR RNA relatively specifically, although it interacts with mRNA with a lower affinity. Based on all of these data, we have proposed that interspersed RNA may be involved in regulating translation by competing with mRNA to interact with certain proteins that can regulate translation.

In vivo storage of XR family interspersed RNA in Xenopus oocytes

Interspersed RNA is an abundant class of cytoplasmic poly(A)+ RNA which contains repetitive elements within mostly heterogeneous single copy sequences. In spite of its quantitative importance in oocytes or eggs (two-thirds of the total poly(A)+ RNA), very little is known about its synthesis, its interaction with other molecules, and its functional significance. Here, we analysed a prevalent family of interspersed RNA (XR family) during Xenopus oogenesis. We found that XR interspersed RNA, unlike extracted interspersed RNA, did not form RNA duplexes in vivo. In small oocytes (stage III), XR RNA interacted with proteins forming rapidly sedimenting ribonucleoprotein particles (RNPs) with a median sedimentation constant of 80S. However, towards the end of oogenesis (stage VI), these XR RNPs changed into smaller particles with a median sedimentation constant of 40S. By analysing the proteins associated with XR RNA sequence, we have identified a 42 kilodalton protein in small oocytes, which was replaced by a 45 kilodalton protein at stage V of oogenesis.

Differential accumulation of mRNA and interspersed RNA during Xenopus oogenesis and embryogenesis

Xenopus oocyte cytoplasmic poly(A)+ RNA has been shown to include two major complex classes: mRNA and interspersed RNA. The former is defined by its translatability, while the latter consists of non-translatable repeat-containing transcripts with unknown functions. In this study we compared the accumulation patterns of total mRNA and a subfamily of interspersed RNA, the XR family (McGrew & Richter, 1989, Dev. Biol. 134, 267-70). The results showed that the XR interspersed RNA level continued to increase throughout oogenesis, while the total mRNA level reached a peak at late stage II and then decreased as much as 40% between stage II and stage VI of oogenesis. In addition we have found that, like mRNA, only about half of the non-translatable XR interspersed RNA underwent deadenylation at oocyte maturation. This result suggested that about half of the interspersed RNA, like certain mRNAs, also contains the U-rich element to protect it from the automatic deadenylation, implying the poly(A) tail of interspersed RNA may play a role during early development.

Sea urchin maternal mRNA classes with distinct development regulation

Previous studies of newly synthesized proteins during early development in sea urchins have revealed several different patterns of synthesis that can be used to predict the existence of mRNA classes with distinct regulatory controls. We have identified clones for abundant maternal mRNAs that are actively translated during early development by screening a cDNA library prepared from polysomal poly(A)+RNA isolated from 2-cell stage (2-hour) Strongylocentrotus purpuratus embryos. Probes prepared from these cDNA clones and several previously characterized maternal mRNA cDNAs were used to compare relative levels of individual mRNAs in eggs and embryos and their translational status at various developmental stages. These abundant mRNAs can be classified into two major groups which we have termed cleavage stage-specific (CSS) and post cleavage stage (PCS) mRNAs. The relative levels of the CSS mRNAs are highest during the rapid cleavage stage and decrease dramatically at the blastula stage (12-hours). In contrast, PCS mRNAs are present at relatively low levels during the rapid cleavage stage and then increase at the blastula stage. Polysome partition profiles reveal that CSS mRNAs are translated more efficiently than PCS mRNAs in the unfertilized egg, at fertilization, and during the cleavage stages. Following the blastula stage, some CSS transcripts move out of polysomes and accumulate as untranslated RNAs, while newly transcribed PCS mRNAs are recruited into polysomes. These data suggest that the rapid cell cycles following fertilization require high levels of specific cleavage stage proteins, and the synthesis of these proteins occurs preferentially over PCS mRNAs.

Analysis of the sequence and expression during sea urchin development of two members of a multigenic family, coding for butanol-extractable proteins

Two cDNA clones related to Paracentrotus lividus butanol-extracted proteins, presumably belonging to cell surface proteins, were isolated by a lambda gt11 expression library of ovary poly A+ RNA. These clones, called bep1 and bep4, of 1,110 and 1,071 bp, respectively, belong to a multigene family. By sequencing analysis, a special structural organization in the coding region is detected. A single copy region is inserted between two regions different from each other but similar in the two clones, which constitute two perfectly preserved domains in the genome and are not always present together in the various members of this gene family. The bep1 and bep4 clones derive from two single genes that are polymorphic in the sea urchin genome. Expression of these clones was studied by Northern blot analysis. Both bep1 and bep4 are transcribed during oogenesis into mRNAs of 1.4 kb, which are stored in eggs and utilized during early embryogenesis. None of these RNAs is, in fact, detectable after the gastrula stage. Moreover, the transcripts of three other members of the family are present in eggs and at the 32 cell stage, but they are also synthesized in the early developmental stages.

Xenopus oocyte poly(A) RNAs that hybridize to a cloned interspersed repeat sequence are not translatable

A cDNA clone encoding an interspersed repeat RNA from Xenopus oocytes was isolated. Each strand of the cDNA clone hybridized to several different oocyte transcripts of diverse size. Many of these transcripts were present in poly(A) RNA at least up to the neurula stage. DNA sequence analysis and hybrid selection and in vitro translation show that molecules of this repeat family are not translatable.

A long, nontranslatable poly(A) RNA stored in the egg of the sea urchin Strongylocentrotus purpuratus

Nontranslatable transcripts containing interspersed repetitive sequence elements constitute a major fraction of the poly(A) RNA stored in the cytoplasm of both the sea urchin egg and the amphibian oocyte. We report the first complete sequence of a representative interspersed maternal RNA transcript, called ISp1. The transcript is about 3.7 kb in length [including poly(A) tail]; and the 5' half consists of a cluster of repetitive sequences, whereas the 3' half is single copy. Other repetitive sequences occur in the 5' and 3' regions flanking the transcription unit. In several cloned alleles, the flanking repetitive and single-copy sequences differ, indicating a high degree of insertional and deletional rearrangement around, as well as within, the transcription unit. No significant open reading frames exist in any region of the ISp1 transcript, nor is it spliced to give rise to translatable mRNA in egg or embryo. A 620-nucleotide repetitive sequence element at the 5' end of the ISp1 transcript is also represented in a large number of other long interspersed maternal poly(A) RNAs. In addition, this sequence appears in a prevalent set of small polyadenylated RNAs about 600-nucleotides in length, which disappear almost completely by the gastrula stage of development. The structural features of the ISp1 RNA uncovered in this work exclude several hypotheses of interspersed maternal poly(A) RNA origin and function.

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.

Sea urchin maternal and embryonic U1 RNAs are spatially segregated in early embryos

We have used in situ hybridization and cell fractionation methods to follow the distribution of U1 RNA and immunofluorescence microscopy to follow the distribution of snRNP proteins in oocytes, eggs, and embryos of several sea urchin species. U1 RNA and U1-specific snRNP antigens are concentrated in germinal vesicles of oocytes. Both appear to relocate after oocyte maturation because they are found primarily, if not exclusively, in the cytoplasm of mature unfertilized eggs. This cytoplasmic residence is maintained during early cleavage and U1 RNA is first detectable in nuclei of micromeres at the 16-cell stage. Between morula and gastrula stages the steady-state concentrations of both RNA and antigens gradually increase in nuclei and decrease in cytoplasm. Surprisingly, analysis of the distribution of newly synthesized U1 RNA shows that it does not equilibrate with the maternal pool. Instead new transcripts are confined to nuclei, while cytoplasmic U1 RNAs are of maternal origin. This lack of equilibration and the conversion of maternal U1 RNAs from nuclear species in oocytes to cytoplasmic in embryos suggests that these RNPs (or RNAs) are structurally altered when released to the cytoplasm at oocyte maturation.

The function of proteins that interact with mRNA

Specific proteins are associated with mRNA in the cytoplasm of eukaryotic cells. The complement of associated proteins depends upon whether the mRNA is an integral component of the polysomal complex being translated, or, alternatively, whether it is part of the non-translated free mRNP fraction. By subjecting cells to ultraviolet irradiation in vivo to cross-link proteins to mRNA, mRNP proteins have been shown to be associated with specific regions of the mRNA molecule. Examination of mRNP complexes containing a unique mRNA has suggested that not all mRNA contain the same family of associated RNA binding proteins. The functions of mRNA associated proteins may include a role in providing stability for mRNA, and/or in modulating translation. With the recent demonstrations that both free and polysomal mRNPs are associated with the cytoskeletal framework, specific mRNP proteins may play a role in determining the subcellular localization of specific mRNPs.

Transcription of a satellite DNA in the newt

Satellite 2 is an abundant, 330-bp tandemly repeated sequence in the genome of the newt, Notophthalmus viridescens. This sequence is distributed throughout the genome on each of the 11 chromosomes. Both strands of satellite 2 are transcribed on the lampbrush chromosomes during oogenesis, probably as a result of readthrough from upstream structural gene promoters. In addition to these heterogeneous nuclear transcripts, satellite 2 is homologous to stable, strand-specific cytoplasmic transcripts in a variety of different tissues. The majority of these transcripts correspond in size to the entire satellite 2 repeat unit, or to whole multiples of the repeat. The transcripts present in the ovary have been sequenced by primer extension and were found to be more homogeneous than eight independently cloned satellite 2 DNA repeats. We propose that the stable cytoplasmic transcripts are encoded by a small subset of genomic satellite 2 sequences.

The neuronal identifier element is a cis-acting positive regulator of gene expression

A middle-repetitive DNA element termed the identifier (ID) sequence, located in introns of postnatal-onset neuronal-specific genes, is transcribed in early postnatal rats by RNA polymerase III (Pol III) specifically in the brain. We show that these Pol III transcripts, although brain specific in vivo, are also expressed in immortalized rodent cell lines in culture. We demonstrate that the ID sequence can act as a positive regulator or enhancer of RNA polymerase II gene expression in cell lines that express these RNAs but not in primary cells in which Pol III transcription of the ID sequence is absent. Thus, ID elements may be positive regulators of postnatal-onset neuronal-specific gene expression.

Stable accumulation of a rat truncated repeat transcript in Xenopus oocytes

To define potential mechanisms of expression of middle-repetitive DNA, Xenopus oocytes were employed to examine the rat type 2 and truncated repeat (TR) elements contained in an intron and in the 3'-flanking region of the rat growth hormone gene. These repeats contain significant sequence and structural homology to tRNA genes and, thus, may represent tRNA pseudogenes. Transcripts from the type 2 elements do not accumulate in the cytosol and are found predominantly in the nucleus, whereas those from TR DNA are expressed in the cytosol of neural and pituitary tissues. In HeLa cell extracts, the rat growth hormone type 2 sequences initiate RNA polymerase III transcription resulting in multiple transcripts of 175-970 nucleotides; some of these also contain TR sequences that are present only as downstream structures since the rat growth hormone-TR DNA lacks promoter activity. In Xenopus oocytes the same template also results in multiple transcripts, but with time a single, homogeneous 73-base RNA preferentially accumulates. This RNA probably arises from larger repetitive DNA transcripts as assessed by the kinetics of its formation, its 5' terminus, and the injection of transcripts generated in HeLa cell-free extracts into the oocytes. Sequence analysis of the 73-base RNA suggests that it is a TR transcripts derived from the TR region with tRNA homology. Stable type 2 transcripts were not detected. Thus, type 2 elements are transcribed in the oocytes, but RNAs from them are degraded whereas discrete TR DNA transcripts can be derived from larger RNA molecules and can accumulate in the cytosol due to their preferential stability. These findings indicate that posttranscriptional control mechanisms can operate to direct differential expression of closely related repetitive DNAs and suggest that structures similar to tRNA contained within the TR sequences may allow them to accumulate preferentially in the cytoplasm.

Evolutionary conservation of DNA sequences expressed in sea urchin eggs and early embryos

DNA sequence divergence measurements indicate that Strongylocentrotus franciscanus is more distinct from S. purpuratus and S. drobachiensis than these two species are from each other, in agreement with paleontological and morphological evidence. The evolutionary divergence of several classes of expressed DNA sequences was compared with that of total single-copy DNA. Between S. franciscanus and S. purpuratus the divergence of cDNA made from gastrula cytoplasmic poly(A)+ RNA is about half that of total single-copy DNA. Similar results were obtained for cDNA made from unfertilized egg poly(A)+ RNA. In contrast, sequences expressed in gastrula nuclear RNA have diverged almost as much as total single-copy DNA.

An ubiquitous interspersed DNA sequence family in an insect

The genome of the African migratory locust, Locusta migratoria (Class Insecta, Order Orthoptera, Family Acrididae) contains an interspersed DNA sequence family, designated the Lm1 family. This family consists of short (approximately 195-bp), widely dispersed, highly reiterated (approximately 6 X 10(5) copies/haploid genome) repeat units, which account for about 2% of the locust genome. Lm1 repeats contain regions that closely resemble internal promoter sequences for RNA polymerase III, and they are structurally very similar to RNA polymerase III templates. Family members are flanked by short direct repeats, and are closely linked to structural genes. These features are reminiscent of the Alu family of man and other repeat sequence families, until now documented only in higher vertebrates.

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

Cap methylation was examined in the early sea urchin embryo. Nucleotide analyses of 3H-methyl methionine-labeled RNA in two-cell embryos and in unfertilized eggs show that fertilization activates the cap methylation of about 10(7) RNA molecules. Greater than 37% of methyl-labeled RNAs following fertilization hybridize with so-called early histone genes H1, H4, and H2B, which encode a subpopulation of the maternal mRNA molecules. Activation of RNA cap methylation is inhibited by aphidicolin, but not by actinomycin D, suggesting that this process is temporally coordinated with DNA replication, but independent of RNA transcription. These results indicate that the translational activation of maternal early histone mRNA during fertilization is a consequence of cap methylation of mRNAs incompletely formed during oogenesis.

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.

Introduction of cloned DNA into sea urchin egg cytoplasm: replication and persistence during embryogenesis

Cloned DNA sequences were introduced into the cytoplasm of unfertilized sea urchin eggs by a simple microinjection technique. Sperm was then added, and development allowed to proceed. If linearized plasmids are injected they form random concatenates, and during the early development of the embryos replicate repeatedly. Eukaryotic sequences are not required for replication of the exogenous DNA. Injected supercoiled DNAs neither ligate nor replicate. Both forms of exogenous DNA persist in the embryo through pluteus stage.

Identification of Xenopus laevis mRNAs with homology to repetitive sequences

Hybrid selection translation experiments have been carried out with genomic and cDNA relatives of two repetitive sequence families. On the basis of the in vitro translation products detected, it was found that transcripts complementary to these repeats are linked to several different mature mRNAs in stage 40 embryos of Xenopus laevis. One repeat hybridizes to mRNAs that direct the synthesis of 17 proteins. The second is present on mRNAs coding for 3 proteins. By estimating the abundance of these proteins among the translation products of total embryonic mRNA, it is inferred that all of the repeat bearing mRNAs are rare, less than one in 20,000 mRNA molecules.

Multiple polymorphic alpha- and beta-tubulin mRNAs are present in sea urchin eggs

Multiple alpha- and beta-tubulin RNAs were found in the mature unfertilized eggs of the sea urchin Lytechinus pictus. The alpha-tubulin RNAs were polymorphic in number, size, and relative amounts in the eggs of different females. Five to seven different size classes [1.75-4.2 kilobases (kb)] were detected on RNA gel blots. All egg preparations contained variable amounts of 1.8- and 2.25-kb beta-tubulin RNAs, and a few of them contained an additional 2.9-kb beta-tubulin RNA. The total amount of alpha-tubulin RNA did not always parallel that of beta-tubulin RNA. A portion of all of the various alpha- and beta-tubulin RNAs were polyadenylylated. RNase H digestions ruled out the possibility that some of these RNAs represented a single transcript bearing different lengths of 3' poly(A). One class of alpha-tubulin RNAs (2.4-2.65 kb) was reduced to 2 kb by RNase H, suggesting the presence of internal oligo(A) regions. All of the egg beta-tubulin RNAs sedimented as free ribonucleoprotein particles. Only a small portion of the 1.75- to 3.6-kb alpha-tubulin RNAs, but most of the 4.2-kb alpha-tubulin RNA, were found on polysomes before fertilization. In the 30-min embryo, small amounts of each of the various alpha- and beta-tubulin RNAs were recruited onto polysomes. Thus, each of the multiple polymorphic alpha- and beta-tubulin RNAs in the egg represent translationally competent mRNA.

opa: a novel family of transcribed repeats shared by the Notch locus and other developmentally regulated loci in D. melanogaster

The principal transcription product of Notch, a locus involved in the neurogenesis of D. melanogaster, is a developmentally regulated poly(A)+ RNA approximately 10.5 kb in length. Analysis of the structure of this RNA has revealed a 93 bp repeated sequence that is shared by many other developmentally regulated transcription units. Nucleotide sequence analysis of the repeat shows an unusual structure consisting predominantly of the triplets CAG and CAA, both of which can code for the amino acid Gln. We present evidence indicating that the Notch repeat is a member of a novel family of repetitive elements, which we term the opa family. Our data suggest that some of these elements may be not only transcribed but also translated. We compare opa with other known transcribed repeats and speculate on its functional significance.

Gene expression during oogenesis and oocyte development in mammals

Mouse oocytes progress through early meiotic prophase during fetal life and reach the diplotene stage by birth. During prepubertal and reproductive life, oocytes are continuously selected to grow from the pool of small primordial oocytes. Growing oocytes reach full size in 2 weeks, and full-grown oocytes are present in rapidly enlarging follicles for about 5 days before meiotic maturation and ovulation. RNA synthesis during early meiotic prophase, as estimated from [3H]uridine incorporation followed by autoradiography and from electron microscopic analysis of nuclear components, proceeds at a moderate rate throughout except for a brief period in early pachytene when synthesis is low or absent. RNA synthesis continues in primordial oocytes at a moderate rate. Incorporation studies, electron microscopic analyses, and particularly measurements of ongoing RNA polymerase activity (completion of initiated chains as analysed in tissue sections) indicate a distinctly increased rate of synthesis during oocyte growth over that of primordial oocytes, followed by a decline in full-grown oocytes. During growth, this rate increases severalfold. The absolute rate of synthesis of heterogeneous nuclear RNA (using rRNA as a standard) during mid-growth is very rapid, but nevertheless still much lower than that in typical lampbrush chromosomes. Most of the hnRNA turns over with a half-life of about 20 min, as is typical in somatic cells. Newly synthesized mRNA-like RNA enters the cytoplasm at about one-half the rate of rRNA, and about one-third of the ribosomes and one-fourth of the mRNA appear in polysomes. In full-grown oocytes, the rate of synthesis falls distinctly, but a significant level of synthesis continues until it essentially ceases at breakdown of the germinal vesicle. During meiotic prophase, chromosomes are most compact at pachytene and unfold lateral projections as RNA synthesis increases in late pachytene-early diplotene. In primordial oocytes, the diplotene state of chromosomes is obvious in most mammals, but in rodents the chromosomes are more evenly dispersed and are said to be in a dictyate state, although they are still presumably in a diplotene configuration. The chromosome core, which is present in leptotene through early diplotene stages, apparently disappears in the dictyate stage.(ABSTRACT TRUNCATED AT 400 WORDS)

Informational content of the echinoderm egg

The sea urchin egg contains a store of mRNA synthesized during oogenesis but translated only after fertilization, which accounts for a large, rapid increase in the rate of synthesis of largely the same set of proteins synthesized by eggs. Starfish oocytes contain a population of stored maternal mRNA that becomes actively translated upon GVBD and codes for a set of proteins distinct from that synthesized by oocytes. The sequence complexity of RNA in echinoderm eggs is about 3.5 x 10(8) nucleotides, enough to code for about 12,000 different mRNAs averaging 3 kb in length. About 2-4% of the egg RNA functions as mRNA during early embryonic development; most of the sequences are rare, represented in a few thousand copies per egg, but some are considerably more abundant. Many of the stored RNA sequences accumulate during the period of vitellogenesis, which lasts a few weeks. The mechanisms of storage and translational activation of maternal mRNA are not well understood. Histone mRNAs are sequested in the egg pronucleus until first cleavage, but other mRNAs are widely distributed in the cytoplasm. The population of maternal RNA includes many very large molecules having interspersed repetitive sequence transcripts colinear with single-copy sequences. The structural features of much of the cytoplasmic maternal RNA is thus reminiscent of incompletely processed nuclear precursors of mRNA. The functional role of these strange molecules is not understood, but many interesting possibilities have been considered. For instance, they may be segregated into different cell lineages during cleavage and/or they may become translationally activated by selective processing during development. Maternal mRNA appears to be underloaded with ribosomes when translated, possibly because the coding sequences are short relative to the size of the mRNA. Most abundant and many rare mRNA sequences persist during embryonic development. The rare sequence molecules are replaced by newly synthesized RNA, but some abundant maternal transcripts appear to persist throughout embryonic development. Most of the proteins present in the egg do not change significantly in mass during development, but a few decline or accumulate substantially. Together, these observations indicate that much of the information for embryogenesis is stored in the egg, although substantial changes in gene expression occur during development.

Co-ordinate control of gene expression. Muscle-specific 7 S RNA contains sequences homologous to 3'-untranslated regions of myosin genes and repetitive DNA

We have cloned and sequenced a complementary DNA copy (pSS48) of a novel muscle-specific, low molecular weight RNA, 7 S RNA, isolated from embryonic chick cardiac muscle cells. The hybridization pattern of plasmid pSS48 DNA to chick genomic DNA suggests that 7 S RNA is derived from the repetitive chick DNA with a repetition frequency of about 300 copies per haploid genome. Under low stringency, pSS48 DNA also hybridizes with high specificity to the single copy gene for chick myosin light chain (MLC) and to myosin heavy chain (MHC), and possibly to other co-ordinately expressed genes for chick muscle proteins. The sequence analysis of recombinant plasmids pSS48, pML10 and pMHC8, for 7 S RNA, MLC mRNA and MHC RNA, respectively, indicated that short nucleotide stretches homologous to 7 S RNA reside in the 3' untranslated regions of the respective genes. The 7 S RNA sequence appears to be highly specific for the chick muscle tissue, since RNA and DNA from several sources did not hybridize to pSS48 DNA. Furthermore, the 7 S RNA-like sequence(s) appears in chick blastodermal cells preferentially earlier than the onset of transcription of genes for major muscle proteins. These results, taken together, suggest a possible function for 7 S RNA in expression of muscle-specific genes during chick development.

Lineage segregation and developmental autonomy in expression of functional muscle acetylcholinesterase mRNA in the ascidian embryo

Acetylcholinesterase is a histospecific marker of cell differentiation occurring only in the muscle and mesenchyme tissues of the ascidian embryo. The distribution of functional mRNA coding for this enzyme has been investigated and it is shown here that only cells of muscle and mesenchyme lineages possess such a template. Blastomeres of four cell lineage quadrants were separated microsurgically from eight-cell-stage embryos of Ciona intestinalis and raised in isolation until muscle development was well advanced. Measurement of enzyme activity in the resulting partial embryos revealed that acetylcholinesterase was limited to descendants of one blastomere pair, the B4.1 blastomeres containing muscle and mesenchyme lineages. To study the tissue distribution of acetylcholinesterase mRNA, RNA from partial embryos was translated in Xenopus laevis oocytes. When oocytes were injected with an appropriate template, they synthesized a biologically active acetylcholinesterase that could be selectively immunopurified with an antiserum to the ascidian enzyme. Under the conditions used the quantity of acetylcholinesterase mRNA was directly related to the enzyme activity in immunoprecipitates. Acetylcholinesterase mRNA was found only in B4.1 lineage partial embryos where it occurred in approximately the same amount as in whole embryos of the same age. Since there is a limited period from gastrulation until the middle tail-formation stage when functional acetylcholinesterase mRNA accumulates, the results of our mRNA distribution experiments strongly suggest that the gene for ascidian acetylcholinesterase is active only in muscle and mesenchyme tissues. The histospecific occurrence of this enzyme apparently does not involve selective, cell-specific control of translation.

Molecular cloning and the complete nucleotide sequence of the creatine kinase-M cDNA from chicken

The nucleotide sequence of creatine kinase-M (CK-M) cDNA clones has been determined. It includes the entire coding region of 381 amino acids in addition to 5' and 3' untranslated regions. A comparison with a partial sequence from rat CK-M reveals 84% nucleotide sequence homology in the coding region but divergence in the 3' untranslated region. The amino acid sequence is 94% conserved between chicken and rat. Hybridization to RNA immobilized on filters indicates homology between the CK-M 3' untranslated region and additional muscle specific RNA species. The coding region hybridizes only to CK-M RNA.

Tissue specificity of 3'-untranslated sequence of myosin light chain gene: unexpected interspecies homology with repetitive DNA

Using the 3' noncoding and coding sequences of chick heart myosin light chain mRNA cloned into Escherichia coli as probes, it was observed that, while the coding sequence shared homology with myosin light-chain mRNAs from other sources, the 3' noncoding sequence was specific for chick heart muscle. This property was used to detect chick heart-specific myosin light-chain gene activity in chick blastoderms of very early developmental stages where cells of different muscle origins cannot be distinguished morphologically. However, in spite of the tissue-specific divergence of the 3' noncoding sequence of myosin light-chain gene, which is present in a single copy in the chick genome, a surprising homology with DNA from such a diverse source like Dictyostelium discoideum was noted. The sequence homologous to chick myosin light-chain DNA was apparently present in a high repetition frequency in the Dictyostelium genome.

Interspersed poly(A) RNAs of amphibian oocytes are not translatable

The poly(A) RNA of the Xenopus oocytes has been shown to include both single copy and interspersed transcripts. Interspersed maternal poly(A) RNAs contain repetitive sequence elements distributed within regions transcribed from single copy sequences. When renatured these RNAs form partially double-stranded RNA networks, and as shown earlier this can be utilized for preparative separation of interspersed maternal transcripts from maternal transcripts that remain single-stranded after renaturation (Anderson et al., 1982). The translational activity of these RNA fractions was tested in vitro, in wheat germ and reticulocyte systems. While the single-stranded fractions supported protein synthesis, the interspersed oocyte RNAs displayed little translational activity. Translational activity was measured in vivo by injection into the Xenopus oocyte. Oocytes previously injected with globin mRNA were injected with increasing amounts of single-stranded, double-stranded, or denatured double-stranded RNA fractions, and the amount of globin synthesis was determined. It was found that single-stranded RNA competes with globin mRNA for the limited translational apparatus of the oocyte, as manifested by a quantitative reduction of globin synthesis. However, globin synthesis was not affected when double-stranded RNA, either in renatured or denatured form, was injected. We conclude that the interspersed RNAs are not translated within the oocyte. The amount of single and double-stranded RNAs loaded onto polysomes in the injected oocytes was also determined. Sixty seven per cent of radio-iodinated single-stranded RNA pelleted with polysomes in injected oocytes, whereas less than 20% of similarly labeled double-stranded RNA pelleted with polysomes. This value is similar to that obtained when partially hydrolyzed RNA is injected, suggesting again that essentially none of the interspersed RNA is translated in vivo. The significance of these findings in relation to translational regulation during oogenesis and early development is discussed.

Delayed accumulation of maternal histone mRNA during sea urchin oogenesis

We have used in situ hybridization and RNA blotting analysis to compare the timing of accumulation of poly(A) and alpha-subtype histone mRNA during oogenesis in the sea urchin Strongylocentrotus purpuratus. In situ hybridization with 3H-poly(U) shows that the content of poly(A) in the developing oocyte increases four- to sixfold during vitellogenesis, implying a similar increase for polyadenylated maternal RNAs. In contrast, both RNA blotting and in situ hybridization demonstrate that there is little, if any, alpha-subtype histone mRNA in large oocytes. These results suggest that these maternal mRNAs accumulate in the pronucleus of the haploid egg after completion of meiotic maturation where they are stored until their release during the breakdown of the pronucleus during prophase.

The 1723 element: a long, homogeneous, highly repeated DNA unit interspersed in the genome of Xenopus laevis

We describe a highly repeated DNA element in the Xenopus laevis genome. This sequence, named the 1723 element, was first identified among sequences that are transcribed during embryonic development. The element is present in about 8500 copies per haploid genome, which together accounts for about 2.4% of the genome. Most copies of the element have highly conserved restriction maps, and are interspersed in the genome. The copies range in size from 6000 to 10,000 base-pairs due to an expandable region that contains variable numbers of a tandemly repeating 183 to 204 base-pair unit. The element is framed by an imperfect 18 base-pair inverted sequence, and inverted repeats of 180 to 185 base-pairs are nearby. Sequence analysis of DNA adjacent to three cloned elements shows that the elements are flanked by 8 base-pair direct repeats. These and other properties of 1723 suggest that it may be transposable.