"Repetitive" DNA in higher organisms

Principles and functions of pericentromeric satellite DNA clustering into chromocenters

Simple non-coding tandem repeats known as satellite DNA are observed widely across eukaryotes. These repeats occupy vast regions at the centromere and pericentromere of chromosomes but their contribution to cellular function has remained incompletely understood. Here, we review the literature on pericentromeric satellite DNA and discuss its organization and functions across eukaryotic species. We specifically focus on chromocenters, DNA-dense nuclear foci that contain clustered pericentromeric satellite DNA repeats from multiple chromosomes. We first discuss chromocenter formation and the roles that epigenetic modifications, satellite DNA transcripts and sequence-specific satellite DNA-binding play in this process. We then review the newly emerging functions of chromocenters in genome encapsulation, the maintenance of cell fate and speciation. We specifically highlight how the rapid divergence of satellite DNA repeats impacts reproductive isolation between closely related species. Together, we underline the importance of this so-called 'junk DNA' in fundamental biological processes.

Satellite-rich DNA in cucumber: hormonal enhancement of synthesis and subcellular identification

Cucumber hypocotyl DNA in neutral CsCl distributes into a mainband comprising 59% of the total, and two large satellite bands which contribute 41% to the DNA pattern. Organelle enrichment studies show that the densities of mitochondrial and chloroplast DNA coincide with those of the satellite bands. At least 12-19% of total cucumber DNA is associated with the cytoplasmic organelles. These values, which are several times larger than those usually quoted for higher plants, are correlated with an unusually low amount of DNA per haploid nucleus in cucumber. Synthesis of the satellite DNAs, as well as mainband DNA, is appreciably stimulated in vivo by application of the plant hormone, gibberellin. Endogenous and hormone-enhanced synthesis of the satellite DNAs is proportionately greater in target tissue showing a high rate of organelle synthetic activity.

Germ line-restricted, highly repeated DNA sequences and their chromosomal localization in a Japanese hagfish (Eptatretus okinoseanus)

The various species of Japanese hagfish, namely, Eptatretus okinoseanus (types A and B), Eptatretus burgeri and Myxine garmani, are known to eliminate a fraction of their chromosomes during early embryogenesis. High molecular weight DNA from germ line cells and somatic cells of these hagfish species was isolated and digested with different restriction enzymes. The DNA fragments were separated by agarose gel electrophoresis. Digestion with BamHI and DraI generated two weak bands and one weak band, respectively, that were estimated to be about 90, and 180 bp and about 90 bp long and were limited to the germ line DNA in both types of E. okinoseanus. DNA filter hybridization experiments showed that the two BamHI fragments and the one DraI fragment were present almost exclusively in the germ line DNA of E. okinoseanus. Thus, these DNA fragments appear to be eliminated during embryogenesis. Moreover, evidence was obtained that these fragments are highly and tandemly repeated. Molecular cloning and sequence analysis revealed that the BamHI fragments are mainly composed of a family of closely related sequences that are 95 bp long (EEEo1, for Eliminated Element of E. okinoseanus 1), and the DraI fragment is composed of another family of closely related sequences that are 85 bp long (EEEo2). The two DNA families account for about 19% of the total eliminated DNA in E. okinoseanus type A. Fluorescence in situ hybridization experiments demonstrated that the two families of DNA are located on several C-band-positive, small chromosomes that are limited to germ cells in both types of E. okinoseanus.

Scanning electron microscopy of mammalian chromosomes from prophase to telophase

Changes in the morphology of human and murine chromosomes during the different stages of mitosis have been examined by scanning electron microscopy. Two important findings have emerged from this study. The first is that prophase chromosomes do not become split into pairs of chromatids until late prophase or early metaphase. This entails two distinct processes of condensation, the earlier one starting as condensations of chromosomes into chromomeres which then fuse to form a cylindrical body. After this cylindrical body has split in two longitudinally, further condensation occurs by mechanisms that probably include coiling of the chromatids as well as other processes. The second finding is that the centromeric heterochromatin does not split in two at the same time as the rest of the chromosome, but remains undivided until anaphase. It is proposed that the function of centromeric heterochromatin is to hold the chromatids together until anaphase, when they are separated by the concerted action of topoisomerase II acting on numerous similar sites provided by the repetitive nature of the satellite DNA in the heterochromatin. A lower limit to the size of blocks of centromeric heterochromatin is placed by the need for adequate mechanical strength to hold the chromatids together, and a higher limit by the necessity for rapid splitting of the heterochromatin at anaphase. Beyond these limits malsegregation will occur, leading to aneuploidy. Because the centromere remains undivided until anaphase, it cannot undergo the later stage of condensation found in the chromosome arms after separation into chromatids, and therefore the centromere remains as a constriction.

Ionizing radiation and genetic risks. II. Nature of radiation-induced mutations in experimental mammalian in vivo systems

This paper reviews data on the nature of spontaneous and radiation-induced mutations in the mouse. The data are from studies using a variety of endpoints scorable at the morphological or the biochemical level and include pre-selected as well as unselected loci at which mutations can lead to recessive or dominant phenotypes. The loci used in the morphological recessive specific-locus tests permit the recovery of a wide spectrum of induced changes. Important variables that affect the nature of radiation-induced mutations (assessed primarily using tests for viability of homozygotes) include: germ cell stage, type of irradiation and the locus. Most of the results pertain to irradiated stem cell spermatogonia. The data on morphological specific-locus mutations show that overall, more than two-thirds of the X- or gamma-ray-induced mutations are lethal when homozygous. This proportion may be lower for those that occur spontaneously, but the numbers of tested mutants are small. For spontaneous mutations, there is evidence for the occurrence of mosaics and for proviral insertions. Most or all tested induced enzyme activity variants, dominant visibles (recovered in specific-locus experiments) and dominant skeletal mutations are lethal when homozygous and this is true of 50% of dominant cataract mutations, but again, the numbers of tested mutants are small. Electrophoretic mobility variants, which are known to be due to base-pair changes, are seldom induced by irradiation. At the histocompatibility loci, no radiation-induced mutations have been recovered, presumably because deletions are incompatible with survival even in heterozygotes. All these findings are consistent with the view that in mouse germ cells, most radiation-induced mutations are DNA deletions. Some mutations (in the morphological specific-locus tests) which had previously been inferred to be deletions on the basis of genetic analyses have now been shown to be DNA deletions by molecular methods. However, the possibility cannot be excluded that at least a small proportion of induced mutations may be intragenic changes. The data on the rates of induction of recessive lethals and of dominant skeletal and dominant cataract mutations (and proportions of the latter two which are homozygous lethal) can be used to estimate the proportions of recessive lethals which are expressed as skeletal abnormalities or cataracts. These calculations show that about 10% of recessive lethals manifest themselves as skeletal and less than 0.2% as cataract mutations.(ABSTRACT TRUNCATED AT 400 WORDS)

Human chromosome-specific repetitive DNA sequences: novel markers for genetic analysis

Two recombinant DNA clones that are localized to single human chromosomes were isolated from a human repetitive DNA library. Clone pHuR 98, a variant satellite 3 sequence, specifically hybridizes to chromosome position 9qh. Clone pHuR 195, a variant satellite 2 sequence, specifically hybridizes to chromosome position 16qh. These locations were determined by fluorescent in situ hybridization to metaphase chromosomes, and confirmed by DNA hybridizations to human chromosomes sorted by flow cytometry. Pulsed field gel electrophoresis analysis indicated that both sequences exist in the genome as large DNA blocks. In situ hybridization to intact interphase nuclei showed a well-defined, localized organization for both DNA sequences. The ability to tag specific human autosomal chromosomes, both at metaphase and in interphase nuclei, allows novel molecular cytogenetic analyses in numerous basic research and clinical studies.

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.

Reiteration frequency of procollagen genes in the guinea pig genome. Collagen genes are not amplified during granuloma fibroblasts differentiation

Procollagen mRNA was purified from collagen synthesizing polysomes obtained from an experimental guinea pig granuloma, and iodinated in vitro. The procollagen 125I-labelled mRNA was hibridized with granuloma and liver guinea pig DNA in vast DNA excess conditions. A Cot 1/2 800-900 mol . s . 1-1 for both tissues was obtained from the hybridization curves. With these results, we could suggest the existence of 11-13 procollagen genes per haploid genome. By the analysis of the hybridization data it was possible to infer that there is no genomic amplification in tissues highly specialized in the synthesis of collagen such as granuloma.

The satellite DNAs of Drosophila simulans

The resolution of antibiotic-CsCl gradients enabled an examination of the satellite DNAs in the nuclear DNA of Drosophila simulans. Of the eight distinct satellite DNAs which were detected, four band at almost the same buoyant density in CsCl but can be resolved in netropsin sulphate-CsCl gradients. Each consists of a repeated sequence which, in five of the satellites, is shown to be arranged in tandem for long regions of the chromosomal DNA. One satellite (1·697 g/ml in CsCl) contains repeated sequences interspersed with other sequences. The satellite DNAs were compared with the satellite DNAs known to be present in the sibling species, D. melanogaster. The two species have different overall complements of satellite DNAs, but one satellite (1·672 g/ml) may be identical.

Restriction enzyme analysis of a highly diverged satellite DNA from Drosophila nasutoides

The satellite II DNA of Drosophila nasutoides is a highly diverged repetitive DNA, showing about 17% base changes between repeat units (Cordeiro-Stone and Lee, 1976). This DNA is cleaved by four different restriction enzymes to produce multimeric fragmentation patterns, indicating that their restriction sites are regularly arranged. Moreover, all four enzymes produce identical fragment lengths, the size of a monomer being 96 base pairs. Such multimeric patterns are expected for a diverged repetitive DNA, since many restriction sequences could have undergone changes during sequence divergence. Further restriction analyses of this DNA by double digestions and cloning reveal that there are three different sequences in satellite II DNA with respect to the presence and the arrangement of various restriction sites (Fig. 7). As an example, one sequence contains many EcoRI sites and fewer HinfI sites (20% of EcoRI sites), which are arranged regularly. These observations suggest that satellite II DNA of D. nasutoides might have evolved through different modes of sequence divergence.

Divergence, differential methylation and interspersion of melon satellite DNA sequences

Melon (Cucumis melo) satellite DNA consists of two components, Q and S, each with a buoyant density in CsCl of 1.707 g/ml, but differing by 9 degrees C in "melting" temperature. These physical properties appear to be in contradiction, since both depend on G + C content. In order to resolve this anomaly, base compositions were directly determined for isolated fractions. the low-"melting" component S contains 41.8% G + C, with 6% of C present as 5-methylcytosine, whereas Q DNA contains 54% G + C, with 41% of C methylated. Analyses of restriction site loss agreed well with the direct determinations of methylation and divergence, and indicated some clustering of methylated sites in Q DNA. Analysis of restricted main-band DNA by hydridization with RNA complementary to Q satellite DNA ("Southern transfer") showed satellite Q tandem arrays interspersed in DNA of main-band density. Sequence divergence and extent of methylation did not appear to depend on whether a repeat array was present as satellite or interspersed in main-band DNA. Hydridization in situ indicated considerable heterogeneity in the genomic proportion of the Q-DNA sequences in melon fruit nuclei, implying over- and under-representation consistent with extensive unequal recombination in satellite Q tandem arrays. The cucumber, Cucumis sativus, contains less than 8% as much Q-homologous DNA per genome as the melon, suggesting rapid evolutionary gain or loss of these tandem repeat sequences.

Highly repetitive component alpha and related alphoid DNAs in man and monkeys

The genomes of Old-World, New-World, and prosimian primates contain members of a large class of highly repetitive DNAs that are related to one another and to component alpha DNA of the African green monkey by their sequence homologies and restriction site periodicities. The members of this class of highly repetitive DNAs are termed the alphoid DNAs, after the prototypical member, component alpha of the African green monkey which was the first such DNA to be identified (Maio, 1971) and sequenced (Rosenberg et al., 1978). The alphoid DNAs appear to be uniquely primate sequences.--From the restriction enzyme cleavage patterns and Southern blot hybridizations under different stringency conditions, the alphoid DNAs comprise multiple sequence families exhibiting varying degrees of homology to component alpha DNA. They also share common elements in their restriction site periodicities (172 . n base-pairs), in the long-range organization of their repeating units, and in their banding behavior in CsCl and Cs2SO4 bouyant density gradients, in which they band within the bulk DNA as cryptic repetitive components.--In the three species from the Family Cercopithecidae examined, the alphoid DNAs represent the most abundant, tandemly repetitive sequence components, comprising about 24% of the African green monkey genome and 8 to 10% of the Rhesus monkey and baboon genomes. In restriction digests, the bulk of the alphoid DNAs among the Cercopithecidae appeared quantitatively reduced to a simple series of arithmetic segments based on a 172 base-pair (bp) repeat. In contrast with these simple restriction patterns, complex patterns were observed when human alphoid DNAs were cleaved with restriction enzymes. Detailed analysis revealed that the human genome contains multiple alphoid sequence families which differ from one another both in their repeat sequence organization and in their degree of homology to the African green monkey component alpha DNA.--The finding of alphoid sequences in other Old-World primate families, in a New-World monkey, and in a prosimian primate attests to the antiquity of these sequences in primate evolution and to the sequence conservatism of a large class of mammalian highly repetitive DNA. In addition, the relative conservatism exhibited by these sequences may distinguish the alphoid DNAs from more recently evolved highly repetitive components and satellite DNAs which have a more restricted taxonomical distribution.

Segmental amplification in a satellite DNA: restriction enzyme analysis of the major satellite of Macropus rufogriseus

The 1.708 g/cc satellite DNA of the red necked wallaby is shown to consist of a number of related families of sequences arranged in tandem arrays. Particular families are subpopulations of other families; their distribution supports a model of successive amplification events during the generation of the satellite. In each amplification episode one 2,500 bp unit is multiplied into a tandemly repeated array of that unit (segmental amplification). The 1.708 g/cc sequences can be detected in related kangaroo species in much reduced amount, and with changes to the long order periodicity of the repeat units.

Fine structure in the thermal denaturation of DNA: high temperature-resolution spectrophotometric studies

Fine structures which appear in the optical melting profile of DNA are examined from both the experimental and theoretical aspects. After a brief historical survey of the DNA melting experiments during the pre-fine-structure era in Section II, the high temperature-resolution experimental techniques which are essential to the investigation of fine structure are described in Section III. Then, the current status of the high-resolution study is reviewed first by a phenomenological description of the melting profile (Section IV) and then of the refolding profile (Section V), where a general idea about the cooperatively melting region and several factors affecting it is given. Sections VI and VII are devoted to the review of current theoretical works. Several well-established theoretical frameworks which correlate the base sequence with the melting phenomena are examined in terms of their rigorousness and usefulness. The molecular thermodynamic parameters concerning the DNA melting which have been evaluated by several research groups are compared and discussed. Finally, in Section VIII, current ideas on the correlation between the fine structure and genetic functions and genetic maps are reviewed. Some future problems relating to the fine structure are also discussed.

Characterization of long and short repetitive sequences in the sea urchin genome

Long and short repetitive sequences were purified from the DNA of Paracentrotus lividus under conditions designed to optimize the yield of complete, end to end sequences. Double-stranded long repeat DNA prepared in this manner ranged in length from approximately 3000 to 15 000 nucleotide pairs with average sizes of approximately 6000 base pairs. In the electron microscope, long repeat DNA was observed to possess continuous sequences that often appeared to be terminated by one or more loops and/or fold backs. Long repeat DNA sequences, resheared to 300 base pairs, were found to have an average melting point identical to that for sheared native DNA. Thus, the reassociated duplexes of long repetitive DNA seem to possess very few mismatched base pairs. Reassociation kinetic analyses indicate that the majority of the long repeat sequences are reiterated only 4--7 times per haploid amount of DNA. Melt-reassociation analyses of short repetitive DNA, at several criteria, support the previously held concept that these sequences belong the sets or families of sequences which are inexact copies of one another. Our studies also support hypotheses suggesting that short repetitive sequences belong to families which may have arisen via distinct salttatory events. The relationships between long and short repetitive DNA sequences are considered with respect to widely held concepts of their sequence organization, evolution, and possible functions within eucaryotic genomes. A model for the possible organization of short repeats within long repetitive DNA sequences is also presented.

Localization of satellite DNAs in the chromosomes of the guinea pig

The in situ hybridization method has been used to investigate the localization of each of the three satellite DNAs present in the genome of the guinea pig. Purified fractions of the satellite DNAs were utilized as templates for synthesis of 3H-labeled complementary RNA (cRNA) by E. coli RNA polymerase, then each cRNA was hybridized to metaphase spreads of embryonic guinea pig cells. The cRNAs of all three satellite DNAs hybridized predominantly to the centromeric region of the chromosomes. The cRNAs of satellite DNAs II and III hybridized to all chromosomes except the Y chromosome. The cRNA of satellite DNA I did not hybridize to the Y chromosome nor to two pairs of small acrocentric chromosomes. Satellite II cRNA hybridized to the telomeric region of chromosomes 3 and 4.

Distribution pattern and enzymic hypermethylation of inverted repetitive DNA sequences in P815 mastocytoma cells

A specific class of DNA sequences, the inverted repetitive sequences, forms a double-stranded structure within a single linear polynucleotide chain in denatured DNA. The reassociation process is unimolecular and occurs very fast. Quantitative analyses have shown that in mouse P815 cells these sequences comprise about 4% of the nuclear DNA and are interspersed within sequences of other degrees of repetitiveness. After labeling the cells with L-[Me-3H]methionine and [14C]deoxycytidine, relative rates of enzymic DNA methylation were computed on the basis of radioactivities found in pyrimidine residues of the nuclear DNA. The results indicate that in P815 cells, DNA of inverted repetitive sequences is methylated to a level about 50% higher than the normal repetitive DNA sequences and to about 300% higher than the unique and intermediary intermediatry sequences. The biological function of the inverted repetitive sequences, as well as of the role of enzymic methylation of DNA remains unknown.

Genetic determination of antibody specificity. Gene translocation and fusion, the molecular basis for the differentiation of the antibody-producing cell

The best system for the study of cell differentiation is a cell which in its differentiated state differs only by one product. This is the case in the immune system. The undifferentiated, but omnipotent stem cell differentiates into a committed B cell which produces only one type of specific antibody out of a million different, genetically fixed possibilities. Gene translocation and fusion is the basis of this differentiation process.

Sequence studies on mouse L-cell satellite DNA by base-specific degradation with T4 endonuclease IV

The base sequence of mouse L-cell satellite DNA was investigated by degradation of the two separated complementary strands with the base specific enzyme, T4 endonuclease IV. Digestion of the heavy strand DNA released a limited number of oligonucleotides which were separated by ionophoresis/homochromatography, isolated, and sequenced by the 'wandering spot' method. The light strand DNA was resistant to digestion with T4 endonuclease IV and no detectable amounts of oligonucleotides were released. The oligonucleotides obtained from the heavy strand were related in sequence, indicating that mouse satellite DNA derived from a short tandemly repeated sequence. The sequence of part of the original repeat unit is proposed to be C-A-T-T-T-T-T-C. Five major oligonucleotides were identified, all of which differ from the proposed original sequence by single base changes. The five major oligonucleotides occur with about equal frequency and together comprise approximately 50% of the oligonucleotides released by T4 endonuclease IV from the heavy strand DNA. In addition to the five major oligonucleotides, several oligonucleotides were found to occur in lesser amounts. Since these oligonucleotides are related to the major oligonucleotides, it is likely that they have arisen from them by mutation.

Isolation of heavy satellite deoxyribonucleic acid from sea-urchin spermatozoa

Two different methods were used to isolate high-molecular-weight heavy satellite DNA from the spermatozoa of the sea-urchin Lytechinus variegratus. Purification of satellite rDNA (ribosomal DNA) by selective denaturation of the spermatozoal DNA followed by a separation of the native and denatured DNA in an aqueous mixture of poly(ethylene glycol)/dextran is affected by the molecular weight of the spermatozoal DNA. Enrichment of satellite rDNA by selective precipitation of main-band DNA by poly-L-lysine is cumbersome but more suitable.

Evolution of a human Y chromosome-specific repeated sequence

The structure and evolution of a repetitive sequence on the human Y chromosome has been studied by restriction enzyme analysis of both total DNA and the isolated sequence. The sequence is shown to cross-hybridize to sequences in female DNA forming unstable duplexes. Mouse/human cell hybrids have been used to investigate the pattern of sequence homology on the X chromosome and some autosomes. We conclude that this sequence is related to human satellite III, but shows considerable differences in structure.

The location of DNA homologous to human satellite III DNA in the chromosomes of chimpanzee (Pan troglodytes), gorilla (Gorilla gorilla) and orang utan (Pongo pygmaeus)

Radioactive RNA with sequences complementary to human DNA satellite III was hybridised in situ to metaphase chromosomes of the chimpanzee (Pan troglodytes), the gorilla (Gorilla gorilla) and the orangutan (Pongo pygmaeus). A quantitative analysis of the radioactivity, and hence of the chromosomal distribution of human DNA satellite III equivalent sequences in the great apes, was undertaken, and the results compared with interspecies chromosome homologies based upon Giemsa banding patterns. In some instances DNA with sequence homology to human satellite III is present on the equivalent ("homologous") chromosomes in identical positions in two or more species although quantitative differences are observed. In other cases there appears to be no correspondence between satellite DNA location and chromosome homology determined by banding patterns. These results differ from those found for most transcribed DNA sequences where the same sequence is located on homologous chromosomes in each species.

Genetic dissection of heterochromatin in Drosophila: the role of basal X heterochromatin in meiotic sex chromosome behaviour

We have examined the female meiotic behaviour of three X-chromosomes which have large deletions of the basal heterochromatin in Drosophila melanogaster. We find that most of this heterochromatin can be removed without substantially altering pairing and segregation of the two Xs. To compare the role of heterochromatin in male meiosis we have constructed individuals which carry two extra identical heterochromatic mini X chromosomes. These minis behave as univalents even though their heterochromatin is known to contain satellite DNA. We conclude therefore that this satellite DNA is not sufficient to allow effectively normal meiotic behaviour. In all other respects our results in the male extend and confirm Cooper's postulate that there exist specific pairing sites in the X heterochromatin. Thus we find no support in either female or male meiosis for the concenpt that satellite DNA is involved in meiotic chromosome pairing of either a chiasmate or an achiasmate kind.

Characterization of distinct segments in mouse satellite DNA by restriction nucleases

The long-range periodicity of mouse satellite DNA has been analyzed by digestion with five restriction nucleases. With all nucleases tested, a major repeat unit approximately 245 nucleotide pairs became apparent. Minor registers of shorter length were also detected. The total number of cleavage sites per haploid genome for each restriction enzyme as well as their positions relative to each other were determined. While endo R-EcoRII was known to cleave all of the satellite DNA, the other four restriction enzymes were found to generate only weak degradation patterns. The results taken together with quantitative analyses of codigestion experiments indicate that the recognition sequences for each of these four nucleases are clustered on separate parts of the satellite DNA. It is concluded that the satellite DNA, which appears homogeneous by digestion with endo R-EcRII, contains distinct segments each susceptible to degradation with one of the other nucleases. These results have certain implications for theories on the evolution of mouse satellite DNA. A simple mechanism of multiplication and divergence by mutation is not sufficient to explain the data. Additional and alternative processes which are relevant to the evolutionary considerations are discussed.