Transcripts from both strands of a satellite DNA occur on lampbrush chromosome loops of the newt Notophthalmus

Potential genetic functions of tandem repeated DNA sequence blocks in the human genome are based on a highly conserved "chromatin folding code"

This review is based on a thorough description of the structure and sequence organization of tandemly organized repetitive DNA sequence families in the human genome; it is aimed at revealing the locus-specific sequence organization of tandemly repetitive sequence structures as a highly conserved DNA sequence code. These repetitive so-called "super-structures" or "higher-order" structures are able to attract specific nuclear proteins. I shall define this code therefore as a "chromatin folding code". Since locus-specific superstructures of tandemly repetitive sequence units are present not only in the chromosome centromere or telomere region but also on the arms of the chromosomes, I assume that their chromatin folding code may contribute to, or even organize, the folding pathway of the chromatin chain in the nucleus. The "chromatin folding code" is based on its specific "chromatin code", which describes the sequence dependence of the helical pathway of the DNA primary sequence (i.e., secondary structure) entrapping the histone octamers in preferential positions. There is no periodicity in the distribution of the nucleosomes along the DNA chain. The folding pathway of the nucleosomal chromatin chain is however still flexible and determined by e.g., the length of the DNA chain between the nucleosomes. The fixation and stabilization of the chromatin chain in the space of the nucleus (i.e., its "functional state") may be mediated by additionally unique DNA protein interactions that are dictated by the "chromatin folding code". The unique DNA-protein interactions around the centromeres of human chromosomes are revealed for example by their "C-banding". I wish to stress that it is not my aim to relate each block of repetitive DNA sequences to a specific "chromatin folding code", but I shall demonstrate that there is an inherent potential for tandem repeated sequence units to develop a locus-specific repetitive higher order structure; this potential may create a specific chromatin folding code whenever a selection force exists at the position of this repetitive DNA structure in the genome.

A novel heterogeneous nuclear RNP protein with a unique distribution on nascent transcripts

Immediately after the initiation of transcription in eukaryotes, nascent RNA polymerase II transcripts are bound by nuclear proteins resulting in the formation of heterogeneous nuclear ribonucleoprotein (hnRNP) complexes. hnRNP complexes from HeLa cell nuclei contain greater than 20 major proteins in the molecular mass range of 34,000-120,000 D. Among these are the previously described A, B, and C groups of proteins (34,000-43,000 D) and several larger, and as yet uncharacterized, proteins. Here we describe the isolation and characterization of a novel hnRNP protein termed the L protein (64-68 kD by mobility in SDS-polyacrylamide gels). Although L is a bona fide component of hnRNP complexes, it also appears to be a different type of hnRNP protein from those previously characterized. A considerable amount of L is found outside hnRNP complexes, and monoclonal antibodies to the L protein also strongly stain unidentified discrete nonnucleolar structures, in addition to nucleoplasm, in HeLa cell nuclei. Interestingly, the same antibodies stain the majority of nonnucleolar nascent transcripts from the loops of lampbrush chromosomes in the newt, but the most intense staining is localized to the landmark giant loops. The L protein is the first protein of giant loops identified so far, and antibodies to it thus provide a useful tool with which to study these unique RNAs. In addition, isolation and sequencing of cDNA clones for the L protein from human cells predicts a glycine- and proline-rich protein of 60,187 D, which contains two 80 amino acid segments only distantly related to the RNP consensus sequence-type RNA-binding domain. The L protein, therefore, is a new type of hnRNP protein.

The nucleoskeleton and the topology of transcription

Transcription is conventionally believed to occur by passage of a mobile polymerase along a fixed template. Evidence for this model is derived almost entirely from material prepared using hypotonic salt concentrations. Studies on subnuclear structures isolated using hypertonic conditions, and more recently using conditions closer to the physiological, suggest an alternative. Transcription occurs as the template moves past a polymerase attached to a nucleoskeleton; this skeleton is the active site of transcription. Evidence for the two models is summarised. Much of it is consistent with the polymerase being attached and not freely diffusible. Some consequences of such a model are discussed.

DNA-binding proteins on lampbrush chromosome loops

When fixed newt lampbrush chromosomes are treated with RNase to remove nascent transcripts and are then probed with radiolabeled single-stranded DNA in 0.1 x SSC, proteins associated with the majority of the lateral loops bind the probe nonspecifically. One or more common hnRNP proteins, several of which are known to bind single-stranded DNA, could be responsible for this generalized binding. In 1.0 x SSC only a relatively small subset of loops continues to bind the probe. In order to characterize this subset of loops, we prepared polyclonal antibodies against DNA-binding proteins initially identified by "Southwestern" analysis. We show by an in situ double labeling experiment that a polyclonal serum raised against gel-eluted histone H1 recognizes the same lateral loops that bind DNA in 1.0 x SSC.

An abundant testis RNA species shows sequence similarity to Y chromosomal and other genomic sites in Drosophila hydei

A cDNA clone bank was constructed from testis poly(A)+ RNA of Drosophila hydei and screened for clones which hybridize to Y chromosomal DNA sequences. The insert of clone cDhT14 hybridizes to a family of repeated DNA sequences with members distributed within the Y chromosome and elsewhere in the genome. This type of sequence has earlier been described as the Y-associated class of DNA. Southern blot analysis of DNA from different wild-type strains of D. hydei suggests that members of the T14 family of repeated DNA sequences are parts of a family of transposable elements. The genomic localization of the T14 family of repeated DNA sequences was revealed by in situ hybridization to metaphase and polytene chromosomes, and to transcripts of Y chromosomal lampbrush loops. Approximately 10-15 members (20%-30%) of the T14 sequence family reside in 8.3 kb PstI restriction fragments. A genomic clone of one of these DNA fragments, DhT14-8.3, hybridizes to transcripts on the Y chromosomal lampbrush loop "cones", and in conventional in situ hybridization experiments to region 12D/13A of the X chromosome and to region 112 of chromosome 5. The cDNA clone cDhT14 represents a part of an abundant testis RNA species of 5.0 kb. This RNA is also present in ovaries and in 0-3 h, 3-6 h and 6-12 h embryos, but less abundantly than in testes. Both the Y chromosomal site of the 8.3 kb PstI fragments and sites elsewhere in the genome are actively transcribed. At least one of the latter genomic sites is transcribed into the 5.0 kb RNA species.(ABSTRACT TRUNCATED AT 250 WORDS)

Extra-ribosomal spacer sequences in Triturus

We show that, in Triturus vulgaris meridionalis, sequences homologous to the rDNA "non-transcribed" spacer (NTS) are clustered at chromosomal loci where they are not associated with 18 S or 28 S rDNA genes: these sequences are referred to as the extra-ribosomal spacer sequences. Genomic clones containing such extra-ribosomal spacer sequences have been isolated. As shown by restriction mapping, these clones appear to consist mostly of repetitive BamHI fragments that are, in turn, internally repetitious and highly homologous to each other. The structure of the clones was confirmed by nucleotide sequence analysis, which also demonstrates the high degree of conservation between the BamHI elements and the homologous NTS sequences. An intriguing 12 base-pair homology between the extra-ribosomal spacer sequences and a Xenopus NTS enhancer sequence is reported. The possibility that a repetitive octanucleotide motif found within the BamHI elements could act as a recombination hotspot by virtue of its similarity with the Escherichia coli chi sequence is discussed.

Heterochromatic DNA in Triturus (Amphibia, Urodela) II. A centromeric satellite DNA

The MspI family of highly repeated sequences is a centromeric satellite DNA representing about 1% of the genome of the Italian smooth newt, Triturus vulgaris meridionalis. We have studied the structure, genomic organization, chromosomal localization and conservation across species of this family. MspI sequences are around 197 bp long, as shown by sequencing of three cloned units. The family is organized in large clusters of tandemly arrayed units, present at almost all the centromeres of T.v. meridionalis, and is well conserved in the T.v. vulgaris subspecies. Conserved MspI sequences are also present in the related species T. helveticus, where they appear to be clustered at the centromeres of only a few chromosomes. MspI sequences are not found in other Triturus species analysed. The correlation of these sequences with the overall distribution pattern of heterochromatin and the extent of their conservation within the genus Triturus, are discussed.

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.

Structure and function of Y chromosomal DNA. II. Analysis of lampbrush loop associated transcripts in nuclei of primary spermatocytes of Drosophila hydei by in situ hybridization using asymmetric RNA probes of four different families of repetitive DNA

pSP64/65 subclones of four different families of repetitive sequences on the Y chromosome of Drosophila hydei were used for in vitro synthesis of labelled RNA. Pairs of RNA probes of opposite strand polarity were employed to analyse RNAs transcribed on, or associated with, various Y chromosomal lampbrush loops in nuclei of primary spermatocytes of D. hydei. The results of RNA filter analysis and in situ hybridization experiments can be generalized as follows: (1) Y-specific transcripts are heterogeneous in length and are synthesized on lampbrush loops. (2) Transcription of tandemly repeated sequences is usually strand specific. (3) Members of the same sequence family can be found in transcripts from different lampbrush loops. (4) Transcripts not coded by the Y chromosome are accumulated on different subregions of Y chromosomal lampbrush loops.

Structure and function of Y chromosomal DNA. I. Sequence organization and localization of four families of repetitive DNA on the Y chromosome of Drosophila hydei

The sequence organization of four different families of Y chromosomal repetitive DNA is characterized at three levels of spatial extension along the Y chromosome of Drosophila hydei. At the lowest level of resolution, DNA blot analysis of Y chromosomal fragments of different lengths and in situ hybridization experiments on metaphase chromosomes demonstrate the clustering of each particular sequence family within one defined region of the chromosome. At a higher level of resolution, family specific repeats can be detected within these clusters by crosshybridization within 10-20 kb long continuous stretches of cloned DNA in EMBL3 phages. At the highest level of resolution, detailed sequence analysis of representative subclones about 1 kb in length reveals a satellite-like head to tail arrangement of family specific degenerated subrepeats as the building scheme common to all four families. Our results provide the first comparative sequence analysis of three novel families of repetitive DNA on the long arm of the Y chromosome of D. hydei. Additional data are presented which support the existence of two related subfamilies of repetitive DNA on the short arm of the Y chromosome.

Transcription of the histone loci on lampbrush chromosomes of the newt Notophthalmus viridescens

We have investigated transcription of the histone gene cluster on lampbrush chromosomes of the newt Notophthalmus viridescens. Clusters of the five histone genes are separated by long tracts of a DNA repeat called satellite 1. Previous in situ hybridization results demonstrated the presence of histone gene coding regions, intergene spacers, and flanking satellite repeats in giant transcription units on lampbrush chromosomes. These results suggested a model in which transcription initiates at histone gene promoters and continues through the rest of the gene cluster into satellite repeats. The readthrough transcription model predicts that spacer regions upstream of the first promoter in the gene cluster should be absent from nascent transcripts on chromosome loops. We have used such upstream spacer probes for in situ hybridization to lampbrush chromosomes. Contrary to our expectation, the results show that upstream spacer regions are transcribed, and indicate that transcription often initiates upstream of the first histone gene promoter. The relationship of giant transcription units in oocyte nuclei to cytoplasmic histone mRNA is discussed.

Cell-type-specific expression of epidermal cytokeratin genes during gastrulation of Xenopus laevis

Analysis of the spatial pattern of expression of embryo-specific epidermal cytokeratin genes in Xenopus laevis shows earliest activity in the animal pole cells of stage-9 blastulae. These genes are transcribed predominantly in the epithelial or outer ectoderm, to a lesser extent in the sensorial or inner ectoderm, and at low levels if at all in other regions of the embryo. In the early gastrula the entire ectoderm, including preneural and preepidermal regions, expresses cytokeratin mRNAs; accumulation of these mRNAs in preneural cells is terminated after contact is made with involuting chordamesoderm. On the basis of this and earlier work (Sargent et al. 1986) we suggest that the pattern of expression of cytokeratin genes in frog embryogenesis is based on prelocalized components modulated by the inductive influence of involuting chordamesoderm. The cytokeratin proteins are deposited in the form of filamentous networks in both layers of the epidermis. In the epithelial layer, a much denser mesh of filaments is facing the outside of the embryo. This polarity is established at the onset of the polymerization of these filaments. Thus, intraembryonic and intracellular localization of keratin gene expression and protein deposition is established at the onset of activation of these genes.

Transcription of a satellite DNA in the newt

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

3B55: a repetitious sequence family which is transcribed and proportionately replicated in germ-line polyploid nuclei of Calliphora erythrocephala

The chromosomes of dipteran polyploid nurse cell nuclei are functionally analogous to the oocyte lampbrush chromosomes of the Amphibia. In investigating the transcriptional and replicative activity of these nuclei in Calliphora erythrocephala we have identified a cloned highly repetitious DNA fragment which shows enhanced transcriptional activity in these cells and different replicative behavior in these germ-line polyploid nuclei as opposed to somatic polytene nuclei. The clone, 3B55, contains a 6.8-kb insert which consists primarily of tandemly repeated 200-bp sequences defined by RsaI sites. From Southern hybridizations to diploid (embryonic) genomic DNA, 3B55-related DNA was calculated to represent a significant fraction of the haploid genome (0.8% or 5000 kb). In situ hybridizations established that these sequences are present in the pericentric regions of four of the six chromosomes. Thus the 3B55 sequences have the properties of a satellite-type DNA family. Quantitation of the 3B55 200-bp monomer (which represents approximately 60% of the genomic 3B55 DNA sequences in all tissues examined) revealed that in somatic polytene salivary gland nuclei, 3B55 DNA is highly under-replicated to give a monomer representation of only 48 +/- 11 kb per haploid genome. However, in germ-line nurse cell nuclei, 3B55 DNA is proportionately replicated to give a monomer genomic representation (3560 +/- 344 kb) equivalent to that of diploid DNA (3011 +/- 202 kb). Transcripts complementary to 3B55 sequences are at least 25 times more abundant in total nurse cell nuclear RNA than in total embryonic nuclear RNA. These findings suggest an association of the 3B55 sequence family with some germ-line specific function.

Heterochromatic DNA in Triturus (Amphibia, Urodela). I. A satellite DNA component of the pericentric C-bands

We have studied the structure, genome organization, chromosomal location, conservation across species and transcription on lampbrush chromosomes, of an AT-rich satellite DNA component of the newt, Triturus vulgaris meridionalis. The satellite (Sat G), originally isolated by gradient centrifugation, represents about 2% of the vulgaris genome and comprises a highly repetitive sequence family (HindIII family), whose monomers have been cloned. The repeat units are about 330 bp long, as measured on gels, and a cloned unit (pTvm1) is 310 bp long, as shown by sequencing. Abundant clusters of the HindIII family sequences are located within the pericentric heterochromatin (i.e. the C-bands placed at both sides of, and at a certain distance from, the centromeres) in most chromosomes. Both the sequence family and its overall pattern of chromosomal distribution are conserved within the genus Triturus, despite a few species-specific differences. The great majority of the HindIII family sequences are unexpressed on lampbrush chromosomes; they reside within pericentric, condensed segments of the chromosome axis ("loopless bars"). Only a few sequences are transcribed on some loops, suggesting that transcription promotion does not depend on the satellite sequences themselves.

A transcribed satellite DNA from the bullfrog Rana catesbeiana

We have cloned and sequenced a 360 bp repeated sequence from genomic DNA of the bullfrog Rana catesbeiana. This sequence, which we call satellite 1, makes up 0.7% of the genome (1.6 X 10(5) repeats) and is scattered throughout the length of all the chromosomes. In situ hybridization with strand-specific probes demonstrated that transcripts from both strands of satellite 1 occur on lamp-brush chromosome loops. We suggest that these transcripts arise by readthrough from upstream structural gene promoters. Sequences that cross-react with satellite 1 were found in genomic DNA of four out of five other Rana species that we tested, but were absent from the DNA of Xenopus, Bombina, and Acris.

Giant readthrough transcription units at the histone loci on lampbrush chromosomes of the newt Notophthalmus

We have studied transcription at the histone loci in oocytes of the newt Notophthalmus viridescens, using in situ hybridization of cloned probes to the nascent RNA on lampbrush chromosome loops. Clusters of the five histone coding sequences are separated by long tracts of a simple sequence DNA, satellite 1. We had previously demonstrated coordinate transcription of histone genes and satellite 1 sequences. We postulated that satellite sequences were transcribed by readthrough from histone gene promoters; that is, transcription initiated at any of the five usual promoters, but did not terminate at the 3' end of the gene. Instead transcription proceeded through downstream sequences in the histone cluster (including spacers and downstream histone genes), and then through the satellite 1 region. Our model led to several specific predictions, in particular that some internal spacer regions between the genes should be well represented in the RNA on loops, that certain sequences should be absent from the loops, and that presence or absence of particular sequences should be correlated with morphological polarity of the transcription unit. We have hybridized ten strand-specific probes to the lamp-brush chromosomes and we find that the patterns of hybridization agree with the readthrough model of transcription.

Strand specific transcription of satellite DNA I in rat ascites hepatoma cells

Rat satellite DNA I was highly expressed in a rat ascites hepatoma cell line, AH60C. The transcripts were found predominantly in the non-polyadenylated fraction of the nuclear RNA. RNA dot blot assay using strand specific probes revealed a strand-selective transcription of the sequence. The structures of cDNA clones isolated on the basis of their cross-hybridization to satellite DNA I were mainly composed of a tandemly repeated array of this sequence.

Centromeric satellite DNA in the newt Triturus cristatus karelinii and related species: its distribution and transcription on lampbrush chromosomes

Two abundant satellite DNA sequences have been identified in and cloned from the DNA of Triturus cristatus karelinii. The smaller of these with a repeat unit of 33 base pairs (bp) is designated TkS1, the larger with 68 bp is designated TkS2. These satellites are also present in DNA from T.c. cristatus, T.c. carnifex and T. marmoratus but in substantially lower copy number. In situ hybridisations to lampbrush chromosomes of T.c. karelinii and T.c. cristatus have shown that the satellites are concentrated in the heterochromatic centromere bars of T.c. karelinii and in a region around the centromere granule in T.c. cristatus. The satellites also bind specifically to the centromere regions of mitotic metaphase chromosomes. They do not bind to the heteromorphic arms of chromosome 1, which have previously been shown to be rich in highly repeated DNA. DNA/RNA-transcript in situ hybrids to lampbrush chromosomes with TkS1 suggest that this sequence is occasionally transcribed on lampbrush loops near the centromeres.

Monoclonal antibodies to lampbrush chromosome antigens of Pleurodeles waltlii

Germinal vesicles of oocytes from Pleurodeles waltlii were used for immunization of BALB/c mice to obtain hybridomas secreting monoclonal antibodies. The hybridomas were screened for reactivity of their antibodies against lampbrush chromosomes of oocytes, as revealed by indirect immunostaining. Antibodies labelling the lampbrush chromosomes were also tested on histological sections of oocytes, embryos, and larvae of Pleurodeles. Characterization of the antigens was accomplished through immunoblotting of two-dimensional electrophoretic gels of germinal vesicle proteins. The ten monoclonal antibodies giving a positive reaction were classed into five groups. Group 1, exemplified by antibody A33, recognizes all the lampbrush chromosome transcribing sites (loops). Moreover, it differentially labels the cell nuclei during embryonic and larval development. Group 2, antibody B71, also stains all the loops of the lampbrush chromosomes, but does not react with cell nuclei of embryos and larvae. Group 3, antibody A1, labels specific loops, some of which are heterozygous in the strain of P. waltlii used. These heterozygosities have allowed us to localize and to characterize a chromosomal segment on bivalent IV which is heteromorphic in the two partners of the bivalent. We suggest that this heteromorphism represents a morphological distinction between Z and W heterochromosomes. Moreover, this antibody reacts with only one transcription unit along a loop that contains several units. Group 4, antibody B24, stains the only two structures in the lampbrush chromosomes of P. waltlii that do not have a loop organization, the mass "M" and the spheres. Group 5, antibody A35, reacts with the chromomeres. The antigens corresponding to antibodies A33 and B24 have been identified as proteins, which have apparent molecular weights of 80 and 104 kilodaltons, respectively. They correspond to proteins abundant in the germinal vesicles. All the antibodies described here cross-react with the lampbrush chromosomes of five other species of Urodeles.

Polyadenylylation of sea urchin histone RNA sequences in transfected COS cells

The region of pSV2neo that encompasses the simian virus 40 early polyadenylylation signal was replaced with a DNA fragment that spans the 3' end of a sea urchin (Psammechinus miliaris) histone H2A gene. This clone, pMK2.H2A(3'), was used to transfect COS cells. RNA analysis revealed that transcripts from pMK2.H2A(3') were polyadenylylated at a site 85 nucleotides downstream from the expected 3' end of mature H2A mRNA. Nucleotide sequencing showed that the site of poly(A) addition was located 10 nucleotides downstream from a cluster of four A-A-U-A-A-A sequences. The lower accumulation of MK2.H2A(3') mRNA, which was 5-10% that of SV2neo mRNA, suggests that the H2A polyadenylylation signal is relatively inefficient. The relationship of the above findings to the 3' end processing of other histone mRNAs is discussed.

Polyadenylation of histone mRNA in Xenopus oocytes and embryos

Oogenesis of amphibians is an atypical situation in which histone mRNA is polyadenylated. The poly(A) tract on H4 mRNA has been examined by S1 nuclease analysis. Throughout oogenesis the poly(A) tract is very short, and nonexistent on some mRNA molecules. The poly(A) tract is completely removed during maturation of the oocyte, and is absent in embryos and cultured cells.

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.

Processing and nucleo-cytoplasmic transport of histone gene transcripts

Precursors of Xenopus and sea urchin histone mRNAs were synthesized in vitro with the SP6 transcription system, and their maturation and nucleo-cytoplasmic transport was studied by frog oocyte injection. 3' processing is most rapid for homologous histone messenger sequences and does not require either genuine 5' or specific 3' ends of the precursor, but capping of the 5' terminus strongly influences the efficiency of 3' processing. No generation of 5' histone mRNA ends can be detected when precursors containing 5' spacer sequence extensions are injected into the oocyte nucleus. This finding may have some implications for the question whether histone gene transcription could be polycistronic. Using a novel oocyte technique, we have separated nuclei from cytoplasm and have studied the time course of exit of the processed RNA from the oocyte nucleus into the cytoplasm. The results suggest that RNA maturation and nucleo-cytoplasmic transport are not temporally coupled processes.

Continuous reorganization leads to extensive polymorphism in a monkey centromeric satellite

Previously we reported the existence of a highly polymorphic satellite, deca-satellite, in the African green monkey genome; deca-satellite probe anneals to complex sets of repeated restriction endonuclease fragments that differ from individual to individual in the monkey population. Here we present experiments aimed at clarifying the structure and organization of deca-satellite sequences and investigating the mechanisms that generate the polymorphisms. Deca-satellite represents less than 1% of the monkey genome but the percentage varies from one monkey to another. The core sequence 5'-C-C-G-G within the ten base-pair deca-satellite repeat unit is well conserved and the central 5'-C-G is sometimes but not always methylated. Restriction endonuclease analysis with BamHI and EcoRI defines separate satellite domains that have evolved in an independent manner. In situ hybridization shows deca-satellite to be located at the centromeric regions of some but not all monkey chromosomes. This location is independently confirmed by a high frequency, in monkey libraries, of segments containing junctions between deca-satellite and alpha-satellite, the main monkey centromeric satellite. The total number of metaphase chromosomes that show centromeric grains after in situ hybridization with a deca-satellite probe varies from one monkey to another. Moreover, in situ hybridization to endoreduplicated diplochromosomes showed that deca-satellite is occasionally distributed asymmetrically on one or the other of the two pairs of sister chromatids in one diplochromosome. This indicates that major reorganization of the satellite can occur frequently in somatic cells. We discuss several possible mechanisms by which deca-satellite sequences could be either amplified or deleted during a single replicative cycle. Also, on the basis of the marked fluidity of deca-satellite abundance and organization and other well-known attributes of centromeric satellites, we suggest that the existence and maintenance of centromeric satellite rests on the role of the tandem repeats themselves and not on any particular nucleotide sequence, repeat length or organization.

Competition between Xenopus satellite I sequences and Pol III genes for stable transcription complex formation

We have constructed hybrid plasmids bearing both Xenopus 5S RNA genes and satellite I sequences in order to test the effect of satellite DNA on 5S gene transcription. Satellite sequences inactivate 5S transcription in both HeLa S100 and Xenopus oocyte microinjection transcription assays. Inactivation of 5S transcription by satellite DNA is observed both in cis and in trans. Transcription of a tRNA gene is also precluded by satellite I DNA. The Xenopus satellite I repeat contains an RNA polymerase III transcription unit which is highly active in both assay systems. This promoter element is 10- to 25-fold more efficient than the 5S gene in transcription competition assays. This quantitative difference in affinity for transcription components may explain the inactivation of 5S transcription by satellite sequences. The satellite I promoter forms stable transcription complexes in vitro which do not dissociate for at least 30 rounds of transcription. Although stable complex formation on the satellite promoter is largely temperature independent over the range of 0-20 degrees, complex formation on both 5S and tRNA genes exhibits a steep temperature dependence characteristic of DNA helix unwinding. The DNA sequence requirements for stable complex formation on 5S genes have been determined using 5' deletion mutants.

Efficient in vitro synthesis of biologically active RNA and RNA hybridization probes from plasmids containing a bacteriophage SP6 promoter

A simple and efficient method for synthesizing pure single stranded RNAs of virtually any structure is described. This in vitro transcription system is based on the unusually specific RNA synthesis by bacteriophage SP6 RNA polymerase which initiates transcription exclusively at an SP6 promoter. We have constructed convenient cloning vectors that contain an SP6 promoter immediately upstream from a polylinker sequence. Using these SP6 vectors, optimal conditions have been established for in vitro RNA synthesis. The advantages and uses of SP6 derived RNAs as probes for nucleic acid blot and solution hybridizations are demonstrated. We show that single stranded RNA probes of a high specific activity are easy to prepare and can significantly increase the sensitivity of nucleic acid hybridization methods. Furthermore, the SP6 transcription system can be used to prepare RNA substrates for studies on RNA processing (1,5,9) and translation (see accompanying paper).

Histone RNA in amphibian oocytes visualized by in situ hybridization to methacrylate-embedded tissue sections

We present an in situ hybridization method for detecting cellular RNAs in tissue sections using methacrylate as the embedding medium. The technique offers the advantage of superior morphological preservation compared with previously published procedures. Since sections can be cut 1 micron or less in thickness, full advantage is taken of the short path length of 3H electrons. Applying this procedure to developing amphibian oocytes, we investigated the accumulation and localization of RNA complementary to the histone genes and their adjacent spacers. Histone RNA begins to accumulate in the cytoplasm of late pachytene-early diplotene oocytes, rapidly reaching a maximum concentration during Dumont stage 1. After this stage the concentration of histone RNA declines. RNA transcribed from histone coding regions is located almost exclusively in the cytoplasm of oocytes. Transcripts of the spacer regions, which are known to be synthesized on oocyte lampbrush chromosomes, do not accumulate in the oocytes. [3H]RNA complementary to U2 small nuclear RNA, used in these experiments as a control, hybridized predominantly to the nucleus of the oocytes.

Minichromosomal repetitive DNA in Trypanosoma cruzi: its use in a high-sensitivity parasite detection assay

We have isolated genomic clones containing members of a tandemly repeated DNA family from Trypanosoma cruzi. This family, which contains a 195-base pair (bp) repeating unit, is the most abundant repetitive DNA in this organism. DNA sequencing analysis of three adjacent tandem repeats as well as two independent nonadjacent repeats showed relatively little sequence heterogeneity. Surprisingly, the three tandem elements contained a 585-bp open reading frame. However, blot hybridization of RNA from epimastigotes as well as blood-form trypomastigotes failed to show evidence for transcription of these sequences. Fractionation of whole T. cruzi DNA in sucrose gradients or in agarose gels followed by hybridization with appropriate radioactive probes showed that the size distribution of DNA bearing the 195-bp repetitive element is distinct from that of kinetoplast DNA as well as from that of DNA bearing tubulin genes. Hybridization of the 195-bp element probe with DNA from six different T. cruzi strains was positive; hybridization with DNA of other protozoa was negative with the single exception of Leptomonas collosoma , which displayed a weak cross-hybridization signal. Clones bearing this repetitive element are shown to be useful as probes for identification and counting of T. cruzi cells by dot-blot hybridization. The sensitivity of this assay permits detection of the DNA of 30 parasites in blood samples.

Methylation of satellite sequences in mouse spermatogenic and somatic DNAs

The distribution of 5-methyl cytosine (5-MeC) residues in a highly repetitive sequence, mouse major satellite, was examined in germinal versus somatic DNAs by digestion with the methylation sensitive isoschizomers Msp I and Hpa II and Southern blot analysis, using a cloned satellite probe. DNA from liver, brain, and a mouse fibroblast cell line, C3H 10T1/2, yielded a multimeric hybridization pattern after digestion with Msp I (and control Eco RI) but were resistant to digestion with Hpa II, reflecting a high level of methylation of the satellite sequences. In contrast, DNA from mature sperm was undermethylated at these same sequences as indicated by the ability of Hpa II to generate a multimeric pattern. DNAs from purified populations of testis cells in different stages of spermatogenesis were examined to determine when during germ cell differentiation the undermethylation was established. As early as in primitive type A, type A, and type B spermatogonia, an undermethylation of satellite sequences was observed. This suggest that this highly specific undermethylation of germ cell satellite DNA occurs very early in the germ cell lineage, prior to entry into meiosis.

Nucleosome arrangement in green monkey alpha-satellite chromatin. Superimposition of non-random and apparently random patterns

We have studied the structure of tandemly repetitive alpha-satellite chromatin (alpha-chromatin) in African green monkey cells (CV-1 line), using restriction endonucleases and staphylococcal nuclease as probes. While more than 80% of the 172-base-pair (bp) alpha-DNA repeats have a HindIII site, less than 15% of the alpha-DNA repeats have an EcoRI site, and most of the latter alpha-repeats are highly clustered within the CV-1 genome. EcoRI and HindIII solubilize approximately 8% and 2% of the alpha-chromatin, respectively, under the conditions used. EcoRI is thus approximately 30 times more effective than HindIII in solubilizing alpha-chromatin, with relation to the respective cutting frequencies of HindIII and EcoRI on alpha-DNA. EcoRI and HindIII solubilize largely non-overlapping subsets of alpha-chromatin. The DNA size distributions of both EcoRI- and HindIII-solubilized alpha-chromatin particles peak at alpha-monomers. These DNA size distributions are established early in digestion and remain strikingly constant throughout the digestion with either EcoRI or HindIII. Approximately one in every four of both EcoRI- and HindIII-solubilized alpha-chromatin particles is an alpha-monomer. Two-dimensional (deoxyribonucleoprotein leads to DNA) electrophoretic analysis of the EcoRI-solubilized, sucrose gradient-fractionated alpha-oligonucleosomes shows that they do not contain "hidden" EcoRI cuts. Moreover, although the EcoRI-solubilized alpha-oligonucleosomes contain one EcoRI site in every 172-bp alpha-DNA repeat, they are completely resistant to redigestion with EcoRI. This striking difference between the EcoRI-accessible EcoRI sites flanking an EcoRI-solubilized alpha-oligonucleosome and completely EcoRI-resistant internal EcoRI sites in the same alpha-oligonucleosome indicates either that the flanking EcoRI sites occur within a modified chromatin structure or that an altered nucleosome arrangement in the vicinity of a flanking EcoRI site is responsible for its location in the nuclease-sensitive internucleosomal (linker) region. Analogous redigestions of the EcoRI-solubilized alpha-oligonucleosomes with either HindIII, MboII or HaeIII (both before and after selective removal of histone H1 by an exchange onto tRNA) produce a self-consistent pattern of restriction site accessibilities. Taken together, these data strongly suggest a preferred nucleosome arrangement within the EcoRI-solubilized subset of alpha-oligonucleosomes, with the centers of most of the nucleosomal cores being approximately 20 bp and approximately 50 bp away from the nearest EcoRI and HindIII sites, respectively, within the 172-bp alpha-DNA repeat. However, as noted above, the clearly preferred pattern of nucleosome arrangement within the EcoRI-solubilized alpha-oligonucleosomes is invariably violated at the ends of every such alpha-oligonucleosomal particle, suggesting at least a partially statistical origin of this apparently non-random nucleosome arrangement.(ABSTRACT TRUNCATED AT 400 WORDS)

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.

Characterization of satellite DNA in Trypanosoma brucei and Trypanosoma cruzi

We have determined the properties of the simple-sequence satellite DNAs from two protozoa, Trypanosoma brucei and Trypanosoma cruzi. The T. brucei satellite DNA contains 29 mol% guanine plus cytosine and is made up of long tandem arrays of a 177 base-pair repeat. Sequence heterogeneity in these repeats is limited and restricted to certain positions as shown by sequence analysis, restriction enzyme digestion and two-dimensional analysis of nucleotides bordering the AluI and HhaI recognition sites in the repeat. The repeat contains two copies of a 19 base-pair sequence differing by a single base-pair substitution and several additional copies of part of this sequence. Sequence variants of the repeat are clustered in the DNA. Satellite DNA is not detectably linked to other DNA and no transcripts of this DNA are found in T. brucei. The T. cruzi satellite DNA repeat is 196 base-pairs long and contains 53 mol% guanine plus cytosine. Direct repetitions longer than eight base-pairs were not observed in the nucleotide sequence of this repeat. The nucleotide sequences of the satellites of T. brucei and T. cruzi are not related. In cell fractionation experiments, the T. brucei and T. cruzi satellite DNAs were recovered from the nuclear fraction. Micrococcal nuclease digestion of nuclear fractions yielded 193 and 197 base-pair nucleosomal oligomers in T. brucei and T. cruzi, respectively; these oligomers contained satellite DNA but not the extranuclear kinetoplast DNA. The 193 base-pair nucleosomal repeat of T. brucei is significantly different from the 177 base-pair satellite repeat. Satellite and nucleosomal repeats are, therefore, not in phase in T. brucei. These satellite DNAs are the first to be observed in protozoa, and we conclude that their properties are similar to those of satellites from animals or plants.

Transcription of repetitive sequences on Xenopus lampbrush chromosomes

We reinvestigated the lampbrush chromosomes of Xenopus laevis and found them well suited for the study or transcription by in situ hybridization to nascent RNA transcripts. Using this technique, we analyzed the transcription of three repetitive sequences that do not show any sequence homology and that differ in their degree of interspersion. We found that they are located on different parts of the chromosomes: two are clustered, one is interspersed. All three of these sequences are transcribed at the lampbrush chromosome stage and transcripts from both strands of each sequence can be detected. The amount of transcription is apparently not proportional to the number of copies of the repetitive sequence at a given chromosomal locus, suggesting that other sequences are involved in the regulation of their transcription.

Location of specific messenger RNAs in Caenorhabditis elegans by cytological hybridization

We have developed an autoradiographic technique for detecting specific Caenorhabditis elegans messenger RNA molecules in situ by hybridization of labeled, cloned DNA probes to fixed tissue sections and squashes of embryos and adults. We report analyses with probes of actin and collagen gene sequences from a C. elegans genomic clone library. Hybridization is RNase sensitive and tissue specific. In adults the actin probe, which recognizes cytoplasmic as well as muscle actin mRNA, hybridizes strongly to muscle and distal gonad (ovary), somewhat less strongly to maturing oocytes, and weakly to intestine. The collagen probe hybridizes weakly to distal gonad and intestine and very strongly to subcuticular tissues, in particular to the hypodermal cells and syncytial cytoplasm of the lateral hypodermal ridges, which are the sites of cuticle synthesis. In embryos, hybridization to squashes indicates that actin message is present at fertilization, decreases during early cleavage, and then increases again during morphogenesis. By contrast, collagen message is absent until the 100-cell stage and then increases rapidly during morphogenesis. The number of cells labeled is consistent with the view that the collagen probe hybridizes to hypodermal precursor cells. We estimate that our present methods can detect messages representing about 0.2% or more of the total mRNA population, and increases in this sensitivity should be possible. Therefore, the cytological hybridization technique should be useful for determining temporal and spatial patterns of specific mRNA distributions during development, at least for abundant and moderately abundant messages.

Unusual domains of human alphoid satellite DNA with contiguous non-satellite sequences: sequence analysis of a junction region

The sequence organization of cloned segments of Human DNA carrying unusual domains of alphoid satellite was studied by restriction mapping, electron microscopy and base sequence analysis. In some cases restriction mapping revealed the absence of the typical 340 bp EcoR 1 dimer, although blot hybridizations showed the extensive presence of alphoid satellite. A variant monomeric construction was demonstrated by DNA sequencing. Furthermore, inverted repeats within these domains were detected by electron microscopy. In one case these were shown to be the result of interruptions in the satellite sequence by members of a family of repetitive, conserved elements.

Tandemly repeated DNA sequences from Xenopus laevis. I. Studies on sequence organization and variation in satellite 1 DNA (741 base-pair repeat)

A family of tandemly repeated sequences, having a basic repeating unit of 741 base-pairs, has been identified in Xenopus laevis DNA and designated satellite 1. Apart from its rather long repeat unit, the characteristics of this DNA appear to be quite similar to those of complex satellite DNAs from other organisms. The nucleotide sequence of a cloned repeat unit shows no evidence of simpler internal repeats, and there is no obvious suggestion of reasonable RNA- or protein-coding regions. Transcripts homologous to this DNA could not be demonstrated in liver, embryo or oocyte RNAs. By blot-hybridization, satellite 1 has been shown to exist in the genome chiefly as tandem repeats of the 741 base-pair sequence. However, there are a number of repeats that differ from the normal sequence (as judged by loss or gain of restriction sites) and some that differ in length. Similar variants are often, but not always, clustered. Characterization of genomic clones of this satellite has confirmed the tandem organization and clustering of variants. The nature of some variants has been elucidated in more detail. Some regions of the basic repeat seem to be more prone to variation than are others.

Post-transcriptional processing of simian virus 40 late transcripts in injected frog oocytes

The capacity of fully grown Xenopus oocytes to process messenger RNA precursors has been assessed using transcripts synthesized from simian virus 40 (SV40) DNA microinjected into the oocyte nucleus. In oocytes, stable transcripts of the SV40 virion protein genes have undergone at least four post-transcriptional maturation steps: cleavage at 3' splice sites, formation of a mature 3' terminus, addition of poly(A), and selective intracellular partitioning, such that only those RNAs with a mature 3' terminus and poly(A) are located in the cytoplasm. Apparently unspliced transcripts with mature 3' termini are transported into the oocyte cytoplasm. A prominent transcript of roughly the full length of SV40 DNA, bearing a 5' terminus in the same region as late mRNA and confined to the nucleus, is found in oocytes injected with SV40 DNA. The possibility that this transcript may serve as a precursor to late mRNA is discussed.

On evolutionarily conserved simple repetitive DNA sequences: do "sex-specific" satellite components serve any sequence dependent function?

The nuclear genomes of eukaryotes contain DNA of varying degrees of repetition. Highly repetitious DNA and simple repetitive sequences as a fraction thereof appear to be distributed in a non-random fashion in the genome. There are arguments for and against functional roles of simple repetitive sequences, and the reasons for their evolutionary conservation are not at all clear. In order to learn more about the biologic role of simple repetitive sequences in the context of their evolutionary history, we report here the following results from studies of sex-specific snake satellite DNA: 1) The snake simple repeat sequence is 5'-GATAGACA-3' and it is strictly conserved throughout vertebrate evolution. 2) The simple repeat sequence is intimately interspersed with single-copy DNA throughout the mouse genome. 3) The simple repeat is transcribed into RNA in several animal systems and it is translatable in bacterial test systems. 4) The simple repeat sequence is sex-specifically arranged in vertebrates. 5) In snake DNA, the simple repeat is adjacent to a single-copy sequence which singles out a male-specific putative mRNA in mouse polysomal poly (A)+ RNA. Thus even if this snake simple repetitive sequence is not involved in a basic cellular function such as sex-determination, it is nevertheless a valuable tool to approach those problems.

An improved in situ hybridization method for the detection of cellular RNAs in Drosophila tissue sections and its application for localizing transcripts of the homeotic Antennapedia gene complex

An improved method for the detection of cellular RNAs in tissue sections has been developed. It involves in situ hybridization of tritium-labeled cloned DNA probes to tissue sections and autoradiography. The method was calibrated by using a cloned DNA probe complementary to transcripts abundant in the midgut cells of Drosophila larvae. The improved method also permitted the detection of these transcripts in sectioned embryos where they are much less abundant. The sensitivity of the method can be approximated by quantifying the signal intensities over the hybridizing embryonic midgut cells relative to the larval midgut cells for which the number of transcripts has been estimated. Based on these calculations we estimate that the method is sensitive enough to detect 100 complementary RNA molecules per cell after 3 days of autoradiographic exposure with a signal-to-noise ratio of 10. The method has been successfully applied to detect transcripts of the homeotic gene Antennapedia. Serial sections allow us to study the spatial pattern of gene expression in the course of development.

Nucleotide sequence of satellite DNA contained in the eliminated genome of Ascaris lumbricoides

Several restriction endonuclease fragments isolated from highly repetitive satellite DNA of the chromatin eliminating nematode Ascaris lumbricoides var. suum have been cloned. Each type of restriction fragment corresponds to a different variant of the same related ancestral sequence. These variants differ by small deletions, insertions and single base substitutions. Restriction and DBM blot analyses show that members of the same variant class are tandemly linked and therefore are physically separated from other variant classes. A comparison of all the determined sequences establishes a 121 bp long and AT rich consensus sequence. There is evidence for an internal short range periodicity of 11 bp length, indicating that the Ascaris satellite initially may have evolved from an ancestral undecamer sequence. The satellite DNA sequences are mostly but not entirely eliminated from the presumptive somatic cells during chromatin diminution. We have no evidence for transcriptional activity of satellite DNA at any stage or tissue analyzed.