Repetitive sequences of the sea urchin genome. III. Nucleotide sequences of cloned repeat elements

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.

Transcripts containing the sea urchin retroposon family 1 (SURF1) in embryos of the sea urchin Anthocidaris crassispina

We isolated two cDNAs, termed D7 and C2 in the present study, from a cDNA library of the 16-cell embryo of the sea urchin Anthocidaris crassispina. The nucleotide sequence was determined completely for D7, and partially for C2. D7 does not have any significant open reading frames. Both D7 and C2 contain a common sequence that is 62% homologous to the sea urchin retroposon family 1 (SURF1). The SURF1 is a short interspersed repetitive element identified from the sea urchin Strongylocentrotus purpuratus, and is reported to be transcribed by RNA polymerase III. The structural feature of D7 and C2, however, suggests that they may be transcribed by RNA polymerase II. RT-PCR analyses revealed that (1) both D7 and C2 transcripts exist as a maternal RNA in the egg, (2) they appear evenly distributed in the 16-cell embryo, and (3) C2 transcripts are present throughout the development up to the gastrula, while D7 transcripts decrease in amount after the early cleavage stage.

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.

A highly polymorphic (ACT)n VNTR (variable nucleotide of tandem repeats) locus inside intron 12 of COL1A2, one of the two genes involved in dominant osteogenesis imperfecta

A new, highly polymorphic, region consisting of variable number of tandem repeats (VNTR) is described that occurs within intron 12 of the COL1A2 gene. This VNTR consists of the trinucleotide ACT repeated from 6 to 12 times. Of the six alleles so far detected four are common in the three major races. The two rare alleles, (ACT)11 and (ACT)12, have been found only in Africans. In addition, a rapid technique has been developed that can be used successfully with very small amounts of even partially degraded DNA, thus allowing the use of this VNTR for forensic applications. Since dominant OI can be due to mutations at either of two loci (COL1A1 and COL1A2) prenatal diagnosis becomes feasible in the majority of the affected families only if a very informative marker is available for both of these genes. This VNTR provides a very powerful marker for COL1A2. In fact the heterozygosity for it ranges from 0.634 to 0.741 with PIC values from 0.562 to 0.696, respectively. Since trinucleotide repeats can be "unstable," and sometimes pathogenic, the unexplained collagenopathies (or suspected collagenopathies) should be analyzed from this point of view.

The mitochondrial plasmid from Neurospora intermedia strain Labelle-1b contains a long open reading frame with blocks of amino acids characteristic of reverse transcriptases and related proteins

We have determined the DNA sequence of the 4070 base pair mitochondrial plasmid from the Labelle-1b strain of Neurospora intermedia. Analysis of the sequence revealed that the plasmid contains a long open reading frame (ORF) that could encode a protein of up to 1151 amino acids. Codon usage in the long ORF shows no clear relationship to Neurospora mitochondrial genes, nuclear genes, nor to the ORF of a different Neurospora mitochondrial plasmid. The long ORF contains regions of similarity to yeast mitochondrial RNA polymerase as well as blocks of amino acids that are characteristic of reverse transcriptases and the ORFs of certain group II mtDNA introns (Michel and Lang, (1985) Nature 316,641). The plasmid gives rise to specific transcripts, some of which may be unit length, and which carry the information for expression of the long ORF. The genetic organization and content of the plasmid suggest that it is related to mobile genetic elements.

Identification of a repeated sequence in the genome of the sea urchin which is transcribed by RNA polymerase III and contains the features of a retroposon

A repeated sequence element which is located about 200 nucleotides upstream from the protein-coding portion of the muscle actin gene (probably within a large 5' intron) in the genome of the sea urchin, Strongylocentrotus purpuratus has been characterized, and shown to contain the sequence features which indicate that it has been transposed by means of an RNA intermediate. This retroposon-like sequence, SURF1-1, is a member of a family which is dispersed and repeated about 800 times in the genome, referred to as SURF1 (sea urchin retroposon family 1). In vitro transcription of this sequence by RNA polymerase III defines a 300 nucleotide transcription unit which is bounded by a short direct repeated sequence. The 3' end of this unit contains a simple 21 nucleotide A+T-rich sequence characteristic of retroponons, and a consensus B box portion of an internal RNA polymerase III promotor is located 60 to 80 nucleotides downstream from the two sites of transcription initiation. This sequence also contains a 40 nucleotide region that is related to several tRNA sequences (containing the B box), and a 79 nucleotide sequence which is homologous to a repeated sequence previously shown to be present within the 3' untranslated portions of the Spec1 and Spec2 mRNAs of this species (1). Analysis of transcripts of this sequence family in RNA from several embryonic stages indicates that its expression is highest at 11 hours postfertilization (about 128 cells) and drops as development proceeds. Furthermore, most or all, transcription of this sequence family in nuclei isolated from 11 hour embryos is by RNA polymerase III, and is from the same strand which is transcribed in vitro.

A second form of the beta subunit of signal-transducing G proteins

A complementary DNA (cDNA) has been isolated that encodes a second form of the beta subunit of signal-transducing guanine nucleotide-binding regulatory proteins (G proteins). The cDNA corresponds to a 1.8-kilobase mRNA, and nucleotide sequence analysis indicates that the encoded polypeptide consists of 340-amino acid residues with a Mr of 37,335. Although the deduced polypeptide is the same size as that reported previously for the beta subunit, 10% of the amino acid residues are different. Furthermore, the 5' and 3' non-translated regions of this cDNA show no significant homology with those reported previously for cDNAs that encode the beta subunit. These data refute prior conclusions that there is only one form of the G protein beta subunit.

Sequence of mRNA coding for bindin, a species-specific sea urchin sperm protein required for fertilization

Bindin, a major protein of the sea urchin acrosome granule, mediates the species-specific adhesion and binding of sperm to egg required to effect fertilization. We report the isolation and sequence of bindin cDNA clones prepared from Strongylocentrotus purpuratus testis RNA. The bindin gene appears to be productively expressed only in males and only in testes. The protein is produced from a 51-kDa precursor, which is subsequently processed to yield the mature 24-kDa bindin protein.

Complete nucleotide and encoded amino acid sequence of a mammalian myosin heavy chain gene. Evidence against intron-dependent evolution of the rod

The complete nucleotide sequence and exon/intron structure of the rat embryonic skeletal muscle myosin heavy chain (MHC) gene has been determined. This gene comprises 24 X 10(3) bases of DNA and is split into 41 exons. The exons encode a 6035 nucleotide (nt) long mRNA consisting of 90 nt of 5' untranslated, 5820 nt of protein coding and 125 nt of 3' untranslated sequence. The rat embryonic MHC polypeptide is encoded by exons 3 to 41 and contains 1939 amino acid residues with a calculated Mr of 223,900. Its amino acid sequence displays the structural features typical for all sarcomeric MHCs, i.e. an amino-terminal "globular" head region and a carboxy-terminal alpha-helical rod portion that shows the characteristics of a coiled coil with a superimposed 28-residue repeat pattern interrupted at only four positions by "skip" residues. The complex structure of the rat embryonic MHC gene and the conservation of intron locations in this and other MHC genes are indicative of a highly split ancestral sarcomeric MHC gene. Introns in the rat embryonic gene interrupt the coding sequence at the boundaries separating the proteolytic subfragments of the head, but not at the head/rod junction or between the 28-residue repeats present within the rod. Therefore, there is little evidence for exon shuffling and intron-dependent evolution by gene duplication as a mechanism for the generation of the ancestral MHC gene. Rather, intron insertion into a previously non-split ancestral MHC rod gene consisting of multiple tandemly arranged 28-residue-encoding repeats, or convergent evolution of an originally non-repetitive ancestral MHC rod gene must account for the observed structure of the rod-encoding portion of present-day MHC genes.

Persistence and integration of cloned DNA in postembryonic sea urchins

Cloned DNA was injected into the cytoplasm of unfertilized sea urchin eggs which were then fertilized and cultured in the laboratory through metamorphosis. The exogenous DNA replicated manyfold and persisted for weeks in a majority of growing larvae, as shown by hydridizing "dot blots" of the DNA of single individuals with appropriate labeled probes. After metamorphosis 5-15% of the juvenile sea urchins retained the exogenous sequences. Genomic integration of the exogenous sequence was observed in the DNA of a postmetamorphosis juvenile.

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.

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.

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.

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.

A small chromatin-associated RNA homologous to repetitive DNA sequences

The chromatins of rat liver and chicken reticulocytes contain a small RNA of identical length (29 nucleotides). This RNA species differs from the degradation products of nuclear RNA present in the chromatin in possessing a free 3'-hydroxyl terminus. It stays associated with chromatin and is not released from the nuclei during the extraction of nuclear ribonucleoprotein particles. This RNA species was purified from the third fraction of non-histone chromosomal proteins eluted from Sephadex G-200 (fraction 3 RNA). When fraction 3 RNA, isolated from rat liver, was used to screen a rat genomic library approximately 3% of the phage plaques hybridized with the RNA. DNA isolated from four randomly selected hybridizing phage clones hybridized with purified 29-nucleotide RNA demonstrating that the sequences present in the four clones represent those of the 29-nucleotide RNA species and not those of minor contaminants. Each of the four clones contained a different amount of sequences complementary to the RNA species 29-nucleotides-long and in each clone the DNA sequences homologous to this RNA were surrounded by different restriction sites. Hybridization of 3'-32P-labeled fraction 3 RNA with blots of total genomic DNA established that some sequences homologous to this RNA are dispersed in the DNA and others are present on one EcoRI restriction fragment, which is approximately 6000 base pairs long. Fraction 3 RNA is not a degradation product of ribosomal or transfer RNA, it is transcribed from middle repetitive DNA and probably originates by specific release during the formation and/or processing of high-molecular-weight transcripts. In normal liver cells its sequences are not released into the cytoplasm.

Organization and evolution of repeated DNA sequences in closely related plant genomes

In common with many other eukaryotic species, the genomes of species in the genus Allium contain a high proportion of repeated DNA sequences, which may be implicated in the considerable differences in genome size that are seen between even very closely related species. The gross organization of repetitive sequences within the genome of Allium sativum and of some other related species has been investigated using DNA/DNA hybridization studies. Such studies show that there has been much modulation in the amounts of different repeated DNA families during the evolution of the genus Allium; these repetitive elements are interspersed in all species with sequences of low repetition. The organization and distribution of one particular repetitive family within the genus has been examined using a cloned hybridization probe. Hybridization of this probe to DNA from related genomes reveals that this element is present in all Allium species examined, but with large-scale modulation of its abundance, and some considerable changes in its sequence environment. The evolution of such genome-specific arrangements of common repetitive elements and the possible mechanisms by which they might be maintained are discussed.

Gene isolation with cDNA probes from identified Aplysia neurons: neuropeptide modulators of cardiovascular physiology

The Aplysia abdominal ganglion neurons, R3-R14, modulate cardiovascular activity. In vitro translations of poly(A)+ RNA from these cells suggest that they contain a prevalent mRNA encoding a 14 kd protein. Utilizing differential screening techniques with 32P-labeled cDNA synthesized from the poly(A)+ RNA of identified neurons, we isolated the corresponding gene. The Aplysia haploid genome contains a single copy of this sequence, which is interrupted by two large introns and spans approximately 7 kb of genomic DNA. The R3-R14 neurons specifically express this gene, resulting in the synthesis of a 1.25 kb mRNA not found in other abdominal ganglion cells or in the head ganglia. The gene was shown to encode a 13.5 kd precursor, which is proteolytically cleaved into at least three peptides with molecular weights of 5.0, 3.3, and 1.3 kd. These peptides and glycine are thought to act as chemical messengers in the central nervous system and peripherally.

Construction of a small Mus musculus repetitive DNA library: identification of a new satellite sequence in Mus musculus

We report the construction of a small library of recombinant plasmids containing Mus musculus repetitive DNA inserts. The repetitive cloned fraction was derived from denatured genomic DNA by reassociation to a Cot value at which repetitive, but not unique, sequences have reannealed followed by exhaustive S1 nuclease treatment to degrade single stranded DNA. Initial characterizations of this library by colony filter hybridizations have led to the identification of a previously undetected M. musculus minor satellite as well as to clones containing M. musculus major satellite sequences. This new satellite is repeated 10-20 times less than the major satellite in the M. musculus genome. It has a repeat length of 130 nucleotides compared with the M. musculus major satellite with a repeat length of 234 nucleotides. Sequence analysis of the minor satellite has shown that it has a 29 base pair region with extensive homology to one of the major satellite repeating subunits. We also show by in situ hybridization that this minor satellite sequence is located at the centromeres and possibly the arms of at least half the M musculus chromosomes. Sequences related to the minor satellite have been found in the DNA of a related Mus species, Mus spretus, and may represent the major satellite of that species.

A study of chromosomal organization of repetitive DNA sequences by in situ hybridization

Chromosomal DNA restriction fragments from Triturus cristatus carnifex, were cloned in pBR322. Five clones containing repetitive DNA sequences were analysed in terms of size, repetition frequencies, GC contents and interspersion patterns. All the data suggest that the cloned sequences are typical for the major repetitive classes found in carnifex and represent members of individual repetitive families. All five cloned sequences hybridize in situ to nascent RNA transcripts on lampbrush loops present in the heteromorphic region of chromosome 1. One of the cloned sequences is interesting in that it shows individual variation. The least repeated sequences are transcribed at many more loci than the more highly repeated sequences and are better represented in the total ovarian RNA.

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

A random primed complementary DNA (cDNA) clone library constructed from total maternal poly(A) RNA of sea urchin eggs was screened with two cloned genomic repetitive sequence probes. Sets of cDNA clones reacting with each of these repetitive sequences were recovered. Most of the cloned transcripts included both single copy and repeat sequence elements. Except for the shared repeat sequence element, both the repetitive and single copy regions of the members of each set of clones failed to crossreact. Single copy probes linked to the repeats on the cloned maternal RNAs are represented in an asymmetric manner. It follows that many different genomic members of a given dispersed repeat sequence family are represented in the maternal RNA. RNA gel blots carried out with several repeat probes display about 10 to 20 prominent maternal poly(A) RNAs containing transcripts of each repetitive sequence family. The interspersed maternal transcripts are 3000 to 15,000 bases in length. Maternal transcripts reacting with single copy probes derived from the cloned cDNAs persist during embryonic development, and in some cases appear to be augmented by similar, newly synthesized embryo transcripts. Two examples were found in which additional transcripts of different length appear at specific developmental stages. The transcribed single copy regions are highly polymorphic in the genomes of different individual sea urchins, and comparisons of closely related sea urchin species showed that both the prevalence and length of specific maternal transcripts change rapidly during evolution. Nucleotide sequences of two homologous repeat elements occurring on different cloned transcripts displayed translation stop codons in every possible reading frame. These repeat sequences display structural features suggesting that there has been evolutionary transposition into transcription units active during oogenesis. The repeat elements and their flanking single copy regions reside either in very long 3' or 5'-terminal sequences, or in unprocessed intervening sequences in the maternal poly(A) RNA. These findings lead us to the proposal that the majority of the cytoplasmic poly(A) RNA in echinoderm eggs and early embryos is similar in form to RNAs that occur in the nucleus rather than to the messenger RNA of later cells.

Mitochondrial DNA sequences in the nuclear genome of Strongylocentrotus purpuratus

Two sea urchin embryo complementary DNA clones representing mitochondrial 16 S ribosomal RNA and cytochrome oxidase subunit I messenger RNA have been characterized. The cloned cDNAs are colinear with sea urchin mitochondrial DNA, and their identification is based on cross-hybridization with known restriction fragments of human mitochondrial DNA, and on nucleotide sequence determinations. The mitochondrial cDNA clones also displayed an unexpected reaction with specific genomic DNA sequences in gel blot hybridizations. Genomic phage lambda recombinants containing sequences hybridizing with the mitochondrial clones were isolated and the arrangement of these sequences was determined. The genomic region studied contains a sequence homologous with the 3' end of the mitochondrial 16 S rRNA gene, flanked on one side by what is possibly a complete copy of the cytochrome oxidase subunit I gene, and on the other by a duplication of a fragment of this gene. The nucleotide sequence divergence between the mitochondrial and nuclear homologues of the cytochrome oxidase subunit I gene varies for different regions of the gene, from about 13% to 25%, while there is about 8% sequence divergence between nuclear and mitochondrial versions of the 3' 16S rRNA sequence. The structure of the genomic mitochondrial sequence homologues indicates that during sea urchin evolution there occurred a germ-line transposition of a fragment of the mitochondrial genome into the nuclear DNA, followed by rearrangements and single nucleotide substitutions.

Association of two different repetitive DNA elements near immunoglobulin light chain genes

Sequence studies of repetitive DNA elements approximately 6 kb 3' of the mouse immunoglobulin CK region gene show that the R element located there (Gebhard et al. (1982) J. Mol. Biol. 157, 453-471) is adjacent to a 500 base pair long element which shows 80% homology to the BAM5 element sequenced by Fanning (Nuc. Acids Res. (1982), 10, 5003-5013). Neither the BAM5 element nor the R element itself is surrounded by a direct repeat, but the composite element (BAM5 + R) is surrounded by a 15 base pair direct repeat (with one mismatch). Direct repeats, consisting of target site sequences that surround a repetitive DNA element, are thought to arise during the insertion of the element at that site. It therefore appears that the BAM5 and R elements interacted and inserted as a linked entity. The existence of other BAM5/R composites throughout the mouse lambda chain locus indicates that BAM5-R cooperation is not a rare event.

Ubiquitous transposon-like repeats B1 and B2 of the mouse genome: B2 sequencing

Mouse genome contains two major families of short interspersed repeats in more than 10(5) copies scattered throughout the whole genome. They are referred to as B1 and B2 sequences since they were first isolated from the genome library by means of a dsRNA-B probe /1/. In this work, two copies of the B2 family were sequenced and compared with the previously sequenced B1 repeat /2/. A B2 ubiquitous repeat is ca. 190 bp long. The members of the family deviate in 3-5% of nucleotides from the consensus sequence. B2 contains regions of homology to the RNA polymerase III split promoter and to 4.5S snRNA I. Both B1 and B2 contain regions which resemble junctions between exons and introns. In contrast to B1, B2 does not contain apparent homologies to papova viral replication origins and a human Alu sequence. One side of the B2 repeat is represented by a very AT-rich sequence (ca. 30 bp long) followed with an oligo (dA) stretch 10-15 nucleotides long. This region of the repeat is the most variable one. The whole unit is flanked with 15-16 bp direct repeats different in sequenced copies of B2. The same is true of some copies of the B1 family. The properties of B1 and B2 repeats suggest that they may represent a novel class of transposon-like elements in eukaryotic genome. A possible role of B-type repeats in genome reorganization, DNA replication and pre-mRNA processing is discussed.

The 3' untranslated regions of two related mRNAs contain an element highly repeated in the sea urchin genome

Two closely related cDNA clones, pSpec1 and pSpec2, specifying two developmentally regulated tissue specific mRNAs from sea urchin embryos were used to probe a sea urchin genomic lambda library. Screening 10,000 phage by plaque hybridization yielded several hundred positive signals. With more stringent wash procedures, only two to three phage were positive. Three of these phage, one isolated by stringent wash procedures and two isolated by standard wash procedures were further investigated by restriction analysis, RNA gel blots, and DNA sequencing. The phage isolated by the stringent wash procedure appears to be a gene coding for the Specl mRNA. The other phage contain only partial homology to pSpec1 and pSpec2, 150 to 200 base pairs of the 3' untranslated region of the Spec1 and Spec2 mRNAs. It is concluded that the Spec1 and Spec2 mRNAs contain a highly repetitive element near their 3' end. The element is present at 2000 to 3000 copies per genome and may be transcribed at some sites other than those coding for the Spec1 and Spec2 genes. The possible function and evolutionary origin of the repetitive element is discussed.

Molecular biology of the sea urchin embryo

Research on the early development of the sea urchin offers new insights into the process of embryogenesis. Maternal messenger RNA stored in the unfertilized egg supports most of the protein synthesis in the early embryo, but the structure of maternal transcripts suggests that additional functions are also possible. The overall developmental patterns of transcription and protein synthesis are known, and current measurements describe the expression of specific genes, including the histone genes, the ribosomal genes, and the actin genes. Possible mechanisms of developmental commitment are explored for regions of the early embryo that give rise to specified cell lineages, such as the micromere-mesenchyme cell lineage.

Molecular structure of maternal RNA

The presence of a stable maternal mRNA population in mature oocytes of many species is well established. In this paper we show that the mature egg contains, in addition to these mature mRNAs, a structurally more complex population of RNA transcripts. This latter class of RNA consists of polyadenylated transcripts of repetitive and nonrepetitive DNA elements covalently linked into long interspersed molecules. As much as seventy percent of the polyadenylated egg RNA of Xenopus laevis and Strongylocentrotus purpuratus is represented in this interspersed population. Most of the nonrepetitive DNA sequences represented in the mature mRNA population are also present in the interspersed RNA. These transcripts have an organization similar to that of somatic cell nuclear RNA. Data are presented that suggests some of these interspersed maternal transcripts are unprocessed precursor-like molecules. Some possible functions of this novel class of RNA during early development are discussed.