Interspersed sequence organization and developmental representation of cloned poly(A) RNAs from sea urchin eggs

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.

Microsatellite loci in wild-type and inbred Strongylocentrotus purpuratus

Strongylocentrotus purpuratus, a major research model in developmental molecular biology, has been inbred through six generations of sibling matings. Though viability initially decreased, as described earlier, the inbred line now consists of healthy, fertile animals. These are intended to serve as a genomic resource in which the level of polymorphism is decreased with respect to wild S. purpuratus. To genotype the inbred animals eight simple sequence genomic repeats were isolated, in context, and PCR primers were generated against the flanking single-copy sequences. Distribution and polymorphism of these regions of the genome were studied in the genomes of 27 wild individuals and in a sample of the inbred animals at F2 and F3 generations. All eight regions were polymorphic, though to different extents, and their homozygosity was increased by inbreeding as expected. The eight markers suffice to identify unambiguously the cellular DNA of any wild or F3 S. purpuratus individual.

Distal cis-acting elements restrict expression of the CyIIIb actin gene in the aboral ectoderm of the sea urchin embryo

The distal region of the S. purpuratus actin CyIIIb gene, between -400 and -1400 nucleotides, contains at least three distinct cis-acting elements (C1R, C1L and E1) which are necessary for correct expression of fusion reporter genes in transgenic sea urchin embryos. The contribution of these elements in the temporal and spatial regulation of the gene was analyzed by single and double site-directed mutagenesis in fusion constructs which carry the bacterial chloramphenicol acetyl transferase (CAT) gene as a reporter. Following microinjection of the transgenes in sea urchin embryos, the activity of the mutants was compared to the wild type in time and space by measuring CAT activity at the blastula and pluteus embryonic stages and by in situ hybridization to the CAT mRNA at pluteus stage. Our results indicate that E1 is involved in the temporal regulation of CyIIIb and that all three elements are necessary and sufficient to confer aboral (dorsal) ectoderm specificity to the proximal promoter. This is achieved by suppressing the promoter's activity in all other tissues by the cooperative interaction of the cis-acting elements. The C1R element, binding site of the nuclear receptors SpCOUP-TF and SpSHR2, is by itself sufficient to restrict expression in the ectoderm, whereas the aboral ectoderm restricted expression requires in addition the presence of both C1L and E1. It is therefore evident, that the actin CyIIIb gene is exclusively expressed in the aboral ectoderm by a combinatorial repression in all other cell lineages of the developing embryo.

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.

Complexity and organization of DNA-protein interactions in the 5'-regulatory region of an endoderm-specific marker gene in the sea urchin embryo

This study concerns the organization of sites of specific DNA/protein interaction within the regulatory domain of the Endo16 gene of Strongylocentrotus purpuratus. Earlier work had displayed a complex pattern of expression of this gene during embryogenesis. Endo16 transcripts are confined to the definitive vegetal plate in blastula stage embryos; at gastrula stage this gene is expressed throughout the archenteron, but later only in the midgut. In this work we exploited the exceptional experimental accessibility of the sea urchin embryo, with respect to both functional assays of gene regulatory systems and to characterization of transcription factors, in order to approach a complete description of potential Endo16 regulatory interactions. Accurate expression of an Endo16 fusion gene was obtained with a 2200-nucleotide (nt) upstream fragment of the gene. We present a map locating high specificity target sites for DNA-binding proteins within the 2200-nt Endo16 regulatory domain, and an assessment of the complexity of the set of putative Endo16 transcription factors that we have been able to recover from 24-h (blastula stage) nuclear extract. Protein binding sites were initially mapped by gel shift reactions carried out on nested sets of end-labeled restriction fragments, and then to finer resolution by oligonucleotide gel shift competitions. Thirty-eight sites of high specificity DNA-protein interaction were thus identified. Appropriate oligonucleotides were then used for partial purification of the DNA-binding proteins by affinity chromatography. DNA-binding proteins specific for each target site were identified by molecular weight, using southwestern blotting procedures and two-dimensional gel shift separations, and by directly renaturing and reacting with oligonucleotide probes specific proteins that had been resolved by SDS-PAGE from selected affinity column fractions. A complete series of gel shift cross-competitions amongst the target sites was carried out. We conclude that nine different protein factors are bound at unique sites within the Endo16 regulatory domain. Multiple target sites for five other proteins account for the remaining binding site locations. The target sites appear to be organized in a sequence of clusters, focused on the unique factors. The high complexity of the Endo16 gene regulatory system may be characteristic for genes that are spatially regulated in early embryonic development.

Highly identical cassettes of gene regulatory elements, genomically repetitive and present in RNA

A region in the first intron of a metallothionein-encoding gene of the sea urchin Strongylocentrotus purpuratus (SpMTA gene) regulates its 5' promoter activity. Within this region is a 290-bp cassette of six sequence motifs that are present in other genes in this species and posited to operate as regulatory elements. The cassette, present at high multiplicity in the genome, was used to screen genomic DNA clones. Of these, six diverse individuals were partially sequenced and found to have segments 94% identical to the 290-bp cassette in the SpMTA gene. Their next 80 bp diverged from the SpMTA sequence but were highly identical among the six non-SpMTA clones and contained an additional regulatory motif. These diverse clones thus contained 370-bp cassettes of an overall 94% sequence identity and an apparent content of seven regulatory elements. The regulatory cassettes were transposon-like, insofar as the termini of the highly identical regions consisted of 24- to 25-bp inverted repeats, bracketed by 6- to 9-bp direct repeats in the divergent regions. In addition to being in transcripts of the SpMTA intron, the cassette was found in other sea urchin embryo poly(A)+ RNAs, in eggs and embryos, and enriched in pluteus ectoderm. The cassette sequence was present in moderate abundance in transcripts in both sense and antisense orientation. We report the presence of a transposon-like cassette of regulatory elements that is also represented in RNA, which potentially could function differently from previously described transposons.

SpCOUP-TF: a sea urchin member of the steroid/thyroid hormone receptor family

Embryonic nuclear proteins from the sea urchin Strongylocentrotus purpuratus bind in vitro to a cis-acting element that lies upstream of the actin gene CyIIIb and consists of two direct repeats homologous to steroid hormone response elements. This sea urchin element is specifically recognized by transcription factor COUP-TF from HeLa cell nuclear extracts as well. A sea urchin gene homologous to the human COUP-TF1 gene was detected by blot hybridization to S. purpuratus genomic DNA. Screening of a genomic DNA library with a human COUP-TF1 cDNA probe produced overlapping genomic clones that carry the S. purpuratus gene. Our results indicate that the sea urchin homologue has a structure similar to the human COUP-TF1 gene, i.e., conserved intron positions characteristic of this subgroup of steroid hormone receptors. Sequencing of the exons that encode the DNA- and ligand-binding domains of the sea urchin protein revealed 96% and 92% amino acid identity to the domains of the human protein, respectively. Transcripts derived from the S. purpuratus COUP-TF homologous gene were detected in ovarian and embryonic RNAs from various stages.

Stage- and adult tissue-specific expression of a homeobox gene in embryo and adult Parechinus angulosus sea urchins

We report the isolation of a gene (PaHbox6), encoding a homeobox-containing protein of the South African sea urchin, Parechinus angulosus. Sequencing identified an Antennapedia-class gene encoding a homeobox that is the homologue of the Hawaiian sea urchin Tripneustes gratilla homeobox gene. Extensive restriction-fragment length polymorphism surrounds the gene. RNase-protection analyses revealed expression of PaHbox6 in mesenchyme blastula embryos at maximal levels of 44 +/- 8 transcripts/embryo. Four adult tissues examined (testes, ovary, intestines, Aristotle's lantern) showed expression of PaHbox6, though at greatly differing levels, with testes highest at eleven transcripts/10 pg RNA. Two transcripts of 5.2 and 5.7 kb were identified in adult tissue.

Two dispersed highly repeated DNA families of Triturus vulgaris meridionalis (Amphibia, Urodela) are widely conserved among Salamandridae

Two BamHI families of repeated sequences were characterized from the genome of the Italian smooth newt, Triturus vulgaris meridionalis (Amphibia, Urodela). The first family, which is divided into subfamilies, consists of tandemly arranged arrays whose basic repeat is around 398 bp long; these arrays are dispersed throughout the entire chromosome sets of the various species of Triturus tested. Moreover the family is widely conserved among Salamandridae, being detected by genomic DNA blotting of Notophthalmus viridescens, Taricha granulosa, Salamandrina terdigitata and Euproctus platycephalus. The second BamHI family is represented by a cloned sequence of 419 bp, which is dispersed in the chromosome set of several species of Triturus. The sequence is also conserved in S. terdigitata and in E. platycephalus but is not detectable in N. viridescens or T. granulosa. The cloned sequence is most probably only part of a longer unit interspersed within the Triturus genome.

Rare maternal mRNAs code for regulatory proteins that control lineage-specific gene expression in the sea urchin embryo

The prevalence of mRNAs coding for the sea urchin embryo regulatory factors P3A1 and P3A2 was measured by single-strand probe excess solution hybridization. P3A1 and P3A2 are not homologous proteins, though they both bind specifically to a particular cis-regulatory sequence. Interaction at this target site is known to be required for lineage-specific expression of an aboral ectoderm-specific gene and probably for several other genes as well. Genome blot hybridizations show that both factors are encoded by single-copy genes. Maternal mRNAs for both factors are present at less than 10(3) molecules per egg, which places them in the rare mRNA class. During development to the mesenchyme blastula stage, the amount of P3A1 mRNA (per embryo) increases severalfold while that of P3A2 remains approximately constant. Specification of the aboral ectoderm founder cells and of their initial patterns of gene expression must occur during early to mid-cleavage stage. Therefore, the regulatory proteins needed for this process must be produced by this stage. We show that the quantities of the P3A proteins that can be synthesized from the numbers of mRNA molecules present in the large blastomeres of the early embryo are sufficient to be functional, because these proteins will be accumulated in the nuclei. Thus maternal P3A1 or P3A2 proteins asre not required, nor were these detected in earlier studies. Furthermore, differential spatial (as well as temporal) distribution of both of these newly synthesized factor species could result from the unequal cleavage pattern utilized in the sea urchin egg.

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.

Expression and structure of the CyIIIb actin gene of the sea urchin Strongylocentrotus purpuratus

The developmental pattern of expression of the Strongylocentrotus purpuratus CyIIIb actin gene was determined by RNA blot hybridizations carried out with a gene-specific probe and total embryonic RNA isolated from various stages of development. The results indicate that the CyIIIb mRNA is not detected in the maternal pool, and, although the gene is activated at the early stages (about 10 hr postfertilization), considerable amounts of mRNA do not accumulate until well into the pluteus stage 3 days later. These results suggest either a post-transcriptional regulatory mechanism that governs early embryonic expression of the CyIIIb actin or a late embryonic transcriptional enhancement of this gene. We present here the complete nucleotide sequence of the CyIIIb gene, which lies within the 10,361 base pairs of the sequenced region. The entire transcription unit is 7,455 nt long and shares structural similarities with the other cytoskeletal-type actin genes from this sea urchin. Sequence comparisons of CyIIIb to the CyIIIa actin gene, to which it is linked, reveals extensive homology even in the introns. The deduced amino acid sequence of the CyIIIb actin shows five amino acid substitutions compared with the CyIIIa actin and nine when compared with the CyI, the endodermal embryonic cytoskeletal-type actin. Five out of these nine amino acid differences occur within a small peptide (position 257 to 267). The 5' flanking sequence of the CyIIIb gene shows a remarkable homology (approximately 75-80%) with the CyIIIa upstream region up to the position -200 and a lack of any obvious similarity further upstream. This observation suggests that the two genes possibly share some common regulatory factors.

Stage- and tissue-specific expression of two homeo box genes in sea urchin embryos and adults

We report the isolation of two different homeo box genes, HB3 and HB4, from the Hawaiian sea urchin Tripneustes gratilla. DNA sequencing revealed a definitive Antennapedia (Antp) class homeo box in each gene. Southern transfer hybridizations showed the genes to be single-copy. A 5.7-kb transcript of the HB3 gene was found in ovary, testis, small intestine and gastrula poly(A)+ RNA. The HB4 gene produces three transcripts. A 3.7-kb and a 4.4-kb transcript are expressed during embryogenesis. A 3.5-kb transcript appears in each of the adult tissues studied. The HB4 gene appears to be the sea urchin cognate of the Drosophila infrabdominal-7 (iab-7) gene, the mouse Hox 1.7 and Hox 3.2 genes and the Xenopus X1Hbox 6 gene. An examination of Antp class homeo box genes in deuterostomes indicates that a chromosomal duplication has taken place in the evolutionary line leading to the vertebrates after the divergence of the echinoderms. Thus, the sea urchin represents the primitive condition.

A gene expressed in the endoderm of the sea urchin embryo

Using a previously cloned, developmentally regulated mRNA sequence expressed predominantly in the endoderm of sea urchin pluteus larvae, we isolated genomic clones and additional cDNA clones to define the gene and the protein it encodes. Nucleic acid sequencing revealed that the gene consists of four exons interrupted by three introns and spans approximately 3600 bp. It encodes a low-molecular-weight protein with polar ends. A stretch of Glu and Asp residues at its carboxyl terminus suggests that it is a nucleic acid-binding protein and a stretch of four Lys residues near the amino terminus suggests a nuclear localization signal.

Cloning of a major repeat DNA sequence from Pyura stolonifera

We have cloned a 147-bp Hind III fragment from a marine ascidian Pyura stolonifera. This sequence is arranged in tandem in arrays up to 20 kb in size and represents more than 5% of the total genomic DNA. The basic 147-bp unit was isolated from Hind III-digested genomic DNA and cloned into M13. Sequence analysis of seven clones revealed that the sequence is AT rich (75%) and can be separated from main band DNA by equilibrium density gradient centrifugation in the presence of the ligand dye Hoechst 33258. The sequence is highly conserved and is changed only by single base substitution mutations in the different clones. Use of this sequence as a probe demonstrated varying degrees of hybridization with DNA isolated from a wide range of other ascidians. Northern blot analysis revealed the presence of RNA hybridizing to the repeat in unfertilized eggs but transcription of this sequence was not evident in the adult organism.

An engrailed class homeo box gene in sea urchins

The homeo box, a conserved DNA element first recognized in Drosophila development-controlling genes, is present in the genomes of many higher metazoan species and provides a valuable probe for the isolation of regulatory genes from diverse phylogenetic groups. We have employed these probes to isolate and study the homeo-box genes in sea urchins. As in other species, the sea urchin homeo boxes fall into at least two classes defined by nucleotide sequence similarity to the homeo boxes of the Drosophila Antennapedia (Antp) and engrailed (en) genes. In this study, we characterize the only detectable sea urchin en class homeo box. Its nucleotide sequence similarity and lack of an intron indicate that it is more closely related to the two mouse en class homeo boxes than to the two Drosophila en class homeo boxes. These relationships are most parsimoniously explained if the single sea urchin en class homeo-box gene represents the primitive condition and the two mouse and the two Drosophila en class homeo-box genes represent independent duplications which occurred in the evolutionary lines leading to the vertebrates and arthropods, respectively. The most abundant en class gene transcripts detected by gel transfer analysis of RNA extracted from sea urchin tissues were found in Aristotle's lantern. Rare transcripts were present in ovary, testis and coelomocytes.

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.

Expression of myosin heavy chain gene in the sea urchin: coregulation with muscle actin transcription in early development

A fragment of a Strongylocentrotus purpuratus (Sp) myosin heavy chain (MHC) gene was isolated from a genomic recombinant DNA library by cross-reaction with a cloned Drosophila melanogaster (Dm) MHC probe. A portion of a 227-nucleotide Sp coding sequence that is included in this fragment predicts a peptide very closely homologous with a region of the Dm sequence. The MHC gene sequence is present in a single copy per haploid Sp genome, and the gene is utilized in adult as well as embryonic muscle. The quantity of MHC transcript was measured in embryos of various stages by single-strand RNA probe excess titration. Transcripts are not observed until postgastrular stages, after which they accumulate rapidly. The time course of accumulation closely parallels that measured earlier for muscle actin message.

Sea urchin actin gene linkages determined by genetic segregation

Genetic linkage between the actin genes of Strongylocentrotus purpuratus was investigated by observing the segregation of restriction fragment length polymorphisms (RFLPs). Specific RFLPs of actin gene pairs CyI/CyIIa and CyIIIa/CyIIIb always cosegregated, confirming the linkage groups CyI-CyIIa-CyIIb previously previously determined by molecular cloning. In contrast, RFLPs of actin genes CyI/CyIIa, CyIIIa/CyIIIb, and M all segregated at random with respect to one another. This demonstrates that the known actin gene clusters CyI-CyIIa-CyIIb, CyIIIa-CyIIIb, and the M actin gene are not closely linked.

Neutral mutations and repetitive DNA

We have previously shown that computer simulations of processes that generate selectively advantageous changes together with random duplications and deletions give rise to genomes with many different genes embedded in a large amount of dispensable DNA sequence. We now explore the consequences of neutral changes on the evolution of genomes. We follow the consequences of sequence divergences that are neutral when they occur in dispensable sequences or extra copies of genes present in multigene families. We find that when divergence occurs at about the same frequency as duplication/deletion events, genomes carry repetitive sequences in proportion to their size. Inspection of the genomes as they evolved showed that multigene families were generated by relatively recent duplications of single genes and so would be expected to be highly homogeneous.

Post-transcriptional restriction of gene expression in sea urchin interspecies hybrid embryos

The synthesis of many paternal species-specific proteins is reduced in all stages of sea urchin interspecies hybrid embryos, due to the reduced amounts of some paternal mRNA species in hybrid embryos compared with the embryos of the paternal species (Tufaro and Brandhorst 1982). Possible explanations for this restriction were tested. Cloned cDNAs were selected that were specific for paternal RNA sequences having reduced amounts (to 2-20% of normal) in hybrid embryos derived from a cross of Stronglyocentrotus purpuratus eggs with Lytechinus pictus sperm. Several of these RNA species are barely detectable in the eggs, but they accumulate extensively (5- to 40-fold) during L. pictus embryogenesis. Thus, the restricted expression of these paternal genes in hybrid embryos is not the result of the persistence of stable maternal mRNA species stored in eggs and not replaced by zygotic transcription. The accumulation of some of these L. pictus transcripts is also reduced in the reciprocal cross (L. pictus eggs X S. purpuratus sperm); therefore, the full expression of these L. pictus genes in hybrid embryos is not dependent on species-specific maternal factors stored in the egg. The transcriptional activity of one such gene was estimated using a run-on assay in isolated nuclei; it is as actively transcribed in hybrid as it is in homospecific embryos, but in hybrid embryos the cytoplasmic transcript accumulates to only 2-15% of the normal level. Sequence analysis indicates that this gene encodes a metallothionein. Mechanisms are discussed that might account for the post-transcriptional restriction of expression of some genes in hybrid embryos.

Developmental and tissue-specific regulation of beta-tubulin gene expression in the embryo of the sea urchin Strongylocentrotus purpuratus

Four beta-tubulin mRNAs in the embryo of the sea urchin Strongylocentrotus purpuratus are transcribed from at least 3 of the 9-12 beta-tubulin genes. A beta 1 tubulin mRNA of 1.8 kb, transcribed from a unique beta 1 gene, is expressed with high specificity in the pluteus ectoderm. Another 1.8-kb mRNA, beta 2, and a 2.5-kb beta 3 mRNA are moderately ectoderm specific. In contrast, a 3.0-kb beta 4 mRNA is highly specific for the endomesoderm tissue fraction. Certain similarities in developmental and tissue-specific expression suggest that these beta-tubulin genes may be related in their mode of regulation to counterparts among the genes for actin, another cytoskeletal protein. Measurements of absolute amounts revealed a distinct developmental profile for each beta-tubulin mRNA. An increase in the total amount of beta-tubulin mRNA in the early blastula was correlated with an increase in transcription rate per nucleus; whereas, later in the mesenchyme blastula stage, the beta-tubulin mRNA level decreased sharply as the rate of beta-tubulin gene transcription on a per embryo basis remained constant. Thus, during development through the blastula stages, there was a switch to a predominantly posttranscriptional regulation of beta-tubulin mRNA expression, probably through a decrease in mRNA stability.

Insertion of an intermediate repetitive sequence into a sea urchin histone-gene spacer

A common polymorphism of the early embryonic histone-gene repeat of Strongylocentrotus purpuratus is a 195-bp insertion within the H4-H2B spacer. The sequence, found as an insert in histone-gene repeats of 6 of 22 individuals screened, is also found at approximately 50 sites elsewhere in the genome of every individual. We compare the sequences of the histone-gene spacers that do and do not contain the insert. The insert is found not to have transposon-like features, and no sequence in the original spacer has been duplicated to flank the insert. There is, however, a hexanucleotide sequence that is repeated three times at one end of the insert, and the element has inserted between direct repeats of 5 bp that were present in the original spacer. One of the copies found outside the histone gene cluster was cloned and sequenced and is compared with the insert. Again, no transposon-like features are evident. Regions flanking the homologous sequence in this clone were used as hybridization probes in whole-genome blots. Results indicate that the 195-bp sequence insert is itself embedded within a larger element that is repeated within the genome. Therefore, only a portion of a larger repetitive sequence has integrated into the histone-gene spacer. The sequence features of the insert, although not typical of mobile elements, may be representative of other illegitimate recombination events.

Sequence organization and developmental expression of an interspersed, repetitive element and associated single-copy DNA sequences in Dictyostelium discoideum

We have examined the genomic organization and developmental expression pattern of a short, transcribed, interspersed repeat element and its associated single-copy sequences. We have previously shown that 1% of the polyadenylated [poly(A)+] RNA from vegetative cells contains sequences that hybridize to this repeat. The complementary RNA is heterogeneous in size, and 90% of its mass hybridizes to single-copy DNA. In this study, we examined a series of genomic DNAs and cDNAs derived from poly(A)+ RNAs which are complementary to the repeat. Comparisons of sequence data from various genomic and cDNA clones indicated that (AAC)n X (GTT)n is the common sequence element. The tandem repeat occurred in approximately 100 short segments (approximately 35 to 150 base pairs) per haploid genome interspersed with single-copy DNA. Probes from regions adjacent to this element hybridized to unique restriction fragments on DNA blots and unique poly(A)+ RNA species on RNA blots. The (AAC)n X (GTT)n sequence was asymmetrically transcribed with only (AAC)n sequences represented in RNA. The repeat was localized within the transcribed regions of several genes and 70 base pairs 5' to the transcription initiation site of another gene. Individual (AAC)n-containing RNAs exhibited a developmental pattern of expression suggestive of the coordinate expression of many AAC gene family members.

Activation of sea urchin actin genes during embryogenesis. Measurement of transcript accumulation from five different genes in Strongylocentrotus purpuratus

The number of molecules of mRNA transcribed from each of five different actin genes are reported for developing embryos of the sea urchin Strongylocentrotus purpuratus. Transcripts of the cytoskeletal actin genes CyI, CyIIa, CyIIb and CyIIIa, and of the muscle actin gene M, were measured in unfertilized egg and embryo RNAs of cleavage, blastula, gastrula and pluteus stages. The measurements were obtained by probe excess titrations of these RNAs, using a set of single-stranded RNA probes each identifying the mRNA transcripts of a specific actin gene. These mRNAs can be identified by their distinct 3' non-translated trailer sequences. We confirm prior observations that the prevalence of actin mRNA in the unfertilized egg is low. Cytoskeletal actin genes CyI and CyIIIa each contribute 1 X 10(3) to 2 X 10(3) maternal mRNA molecules, and CyIIb contributes less than 2 X 10(2) mRNA molecules, while no detectable maternal mRNAs derive from cytoskeletal actin gene CyIIa or the muscle actin gene M. During certain periods of development, transcripts derived from the individual cytoskeletal actin genes accumulate rapidly, with kinetics specific to each mRNA. Transcripts of the muscle actin gene are absent until after gastrulation, when the initial muscle progenitor cells are formed. At late stages of development, each of the five genes studied is represented by 10(4) to 10(5) mRNA molecules per embryo. The present measurements permit calculation of the levels of each actin mRNA species in the particular cell types in which each gene functions in the fully differentiated embryo.

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.

Sequence organization and developmental expression of an interspersed, repetitive element and associated single-copy DNA sequences in Dictyostelium discoideum

We have examined the genomic organization and developmental expression pattern of a short, transcribed, interspersed repeat element and its associated single-copy sequences. We have previously shown that 1% of the polyadenylated [poly(A)+] RNA from vegetative cells contains sequences that hybridize to this repeat. The complementary RNA is heterogeneous in size, and 90% of its mass hybridizes to single-copy DNA. In this study, we examined a series of genomic DNAs and cDNAs derived from poly(A)+ RNAs which are complementary to the repeat. Comparisons of sequence data from various genomic and cDNA clones indicated that (AAC)n X (GTT)n is the common sequence element. The tandem repeat occurred in approximately 100 short segments (approximately 35 to 150 base pairs) per haploid genome interspersed with single-copy DNA. Probes from regions adjacent to this element hybridized to unique restriction fragments on DNA blots and unique poly(A)+ RNA species on RNA blots. The (AAC)n X (GTT)n sequence was asymmetrically transcribed with only (AAC)n sequences represented in RNA. The repeat was localized within the transcribed regions of several genes and 70 base pairs 5' to the transcription initiation site of another gene. Individual (AAC)n-containing RNAs exhibited a developmental pattern of expression suggestive of the coordinate expression of many AAC gene family members.

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.

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.

Structural and transcriptional properties associated with a member of a new family of conserved short dispersed repeated elements in human DNA

The sequence of a 500-bp segment of human DNA containing a member of the 'A3' family of dispersed repeated elements, a family hitherto uncharacterized in human or rodent DNAs, is presented. The repeated element maps to a region of 270 bp, within which the most notable features are 17-mer direct repeats separated by 190 bp. A probe containing the repeated element, together with flanking single-copy DNA illuminates a series of multiple bands in blot transfers of restriction digests of human, mouse and hamster DNAs. However, the flanking single-copy DNA hybridizes to human, but not to rodent DNA. The same probe illuminates homologous transcripts occurring in a single size class of 0.8 kb in total RNA from a variety of human and mouse cells, levels of which vary approx. 100-fold in the tissues analyzed. Poly(A)+ RNAs from EJ-transformed 3T3 cells and mouse fibrosarcomas have been analysed and found also to contain an homologous 0.8-kb transcript.

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.

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.

Control of neuronal gene expression

Some 30,000 genes are expressed exclusively in the rat brain, many of which contain a genetic element called an identifier sequence located in at least one of their introns. The identifier sequences are transcribed by RNA polymerase III exclusively in neurons to produce two RNA species, BC1 and BC2, of 160 and 100 to 110 nucleotides. This transcriptional event may define regions of chromatin that contain neuronal-specific genes and may poise these genes for transcription by polymerase II by rendering the gene promoters accessible to soluble trans-acting molecules.

Insertion of a short repetitive sequence (D88I) in a sea urchin gene: a typical interspersed repeat?

A comparison has been made between the Sp88 gene regions of the DNAs of the sea urchins Strongylocentrotus purpuratus (Sp.) and Strongylocentrotus drobachiensis (Sd.). Examination of the 3' terminal part of the transcribed region revealed a short repetitive sequence present in Sd. but absent from Sp. A 12-nucleotide sequence present once in Sp. is almost perfectly duplicated at both ends of the repeat in Sd., suggesting that a mobile repeat was inserted in the Sd. genome. Other members of this family of repeated sequences occur in many interspersed locations in the genomes of both species. Except for the insertion duplication, the inserted sequence lacks direct or reverse repeats.

Regulation of cytoplasmic mRNA prevalence in sea urchin embryos. Rates of appearance and turnover for specific sequences

Complementary DNA clones representing cytoplasmic poly(A) RNAs of sea urchin embryos were hybridized with metabolically labeled cytoplasmic RNA preparations and the rates of appearance and of decay for each transcript species were determined at the blastula-gastrula stage of development. The prevalence of the transcripts chosen for this study ranged, on average, from about one molecule per cell to a few hundred molecules per cell. The embryos were labeled continuously for 18 hours with [3H]guanosine, beginning at 24 hours post-fertilization. The amount of cytoplasmic [3H]poly(A) RNA that hybridized to each cloned sequence was determined and the specific activity of the [3H]GTP pool was measured in the same embryos. Rate constants for the entry of each transcript species into the cytoplasm, and for its decay were extracted from these data. The embryo transcript species identified by the cloned probes displayed a range of stabilities. Half-lives of only a few hours were measured both for a very rare sequence and for a moderately prevalent sequence. Other newly synthesized transcripts, including sequences that first appear during embryonic development, as well as sequences also represented in maternal RNA, are far more stable. We conclude that cytoplasmic RNA turnover rate is a major variable in the determination of the cytoplasmic level of expression of embryo genes. The entry rates of the transcripts into the cytoplasm also varied, from a few molecules per embryo per minute to several hundred, depending on the sequence. By comparing the mass of transcripts of a given sequence in the embryo to the mass of transcripts of that sequence accumulating as a result of new synthesis, the point at which embryo transcription accounts for the major fraction of the cytoplasmic molecules could be estimated. This calculation showed that for some sequences maternal transcripts persist well beyond gastrulation, while other embryo poly(A) RNA species are largely the product of transcription in the embryo nuclei from the blastula stage onwards. There is no single stage at which all maternal transcripts are suddenly replaced by newly synthesized embryo transcripts. Primary transcription rates were measured for two sequences by determining accumulation of label in these RNA species soon after addition of [3H]guanosine to the cultures. Comparing these rates to the cytoplasmic entry rates, we did not detect a significantly greater nuclear transcription of the sequence homologous to the cloned probe.

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.

Sea urchin actin gene subtypes. Gene number, linkage and evolution

The actin gene family of the sea urchin Strongylocentrotus purpuratus was analyzed by the genome blot method, using subcloned probes specific to the 3' terminal non-translated actin gene sequence, intervening sequence and coding region probes. We define an actin gene subtype as that gene or set of genes displaying homology with a given 3' terminal sequence probe, when hybridized at 55 degrees C, 0.75 M-Na+. By determining the often polymorphic restriction fragment band pattern displayed in genome blots by each probe, all, or almost all of the actin genes in this species could be classified. Our evidence shows that the S. purpuratus genome probably contains seven to eight actin genes, and these can be assigned to four subtypes. Studies of the expression of the genes (Shott et al., 1983) show that the actin genes of three of these subtypes code for cytoskeletal actins (Cy), while the fourth gives rise to a muscle-specific actin (M). We denote the array of S. purpuratus actin genes indicated by our data as follows. There is a single CyI actin gene, two or possibly three CyII genes (CyIIa, CyIIb, and possibly CyIIc), three CyIII actin genes (CyIIIa, CyIIIb, CyIIIc), and a single M actin gene. Comparative studies were carried out on the actin gene families of five other sea urchin species. At least the CyIIa and CyIIb genes are also linked in the Strongylocentrotus franciscanus genome, and this species also has a CyI gene, an M actin gene and at least two CyIII actin genes. It is not clear whether it also possesses a CyIIc actin gene, or a CyIIIc actin gene. The genome of a more closely related congener, Strongylocentrotus dröbachiensis, includes 3' terminal sequences suggesting the presence of a CyIIc gene. In S. franciscanus and S. dröbachiensis the first intron of the CyI gene has remained homologous with intron sequences of both the CyIIa and CyIIb genes, indicating a common origin of these three linked cytoskeletal actin genes. Of the four S. purpuratus 3' terminal subtype probe sequences only the CyI 3' terminal sequence has been conserved sufficiently during evolution to permit detection outside of the genus Strongylocentrotus. An unexpected observation was that a sequence found only in the 3' untranslated region of the CyII actin gene in the DNA of S. dröbachiensis and S. purpuratus is represented as a large family of interspersed repeat sequences in the genome of S. franciscanus.

Transcripts regulated during normal embryonic development and oncogenic transformation share a repetitive element

We have previously isolated cDNA clones homologous to mRNAs present at elevated levels in transformed mouse fibroblasts. Clones of Set 1 contain a dispersed repetitive element present thousands of times in the mouse genome. This repeat identifies in mouse embryos a large number of transcripts that are quantitatively regulated during development. At maximal expression these RNAs constitute between 1% and 3% of polyadenylated RNA. A pattern of Set 1-related transcripts very similar to that observed in midgestation embryos is found in pluripotential EC and EK cell lines, and the abundance of these RNAs decreases upon differentiation in vitro. However, the F9 line of EC cells, which has a more restricted developmental capacity, exhibits a much simpler pattern of transcripts containing the Set 1 repeat.

An unusual accumulation of repetitive sequences in the rat genome

We have found in the rat genomic DNA a fragment 1300 bp long, containing an unusual concentration of members of different repetitive families. Three different repeats were noticed. An Alu-like repeat, homologous to the mouse B1 sequence, was followed by a fragment containing alternating purine-pyrimidine bases as in Z-DNA. Finally, a third repeat was identified, containing 38 TAGA tetranucleotides as described for reptile DNA.

Transcripts of three mitochondrial genes in the RNA of sea urchin eggs and embryos

cDNA clones representing mitochondrial 16 S rRNA, and mRNAs for cytochrome oxidase I and an unidentified reading frame were used to measure the prevalence and stability of these transcripts in gastrula stage embryos. The 16 S rRNA is the most prevalent embryo poly(A) RNA, and is synthesized about four times more rapidly than is the mRNA for cytochrome oxidase. The relative prevalence of the two mRNAs is largely determined by their turnover rates.