Highly repeated sequences in mammalian genomes

Molecular evolution of centromere-associated nucleotide sequences in two species of canids

The major centromeric satellite nt sequences present in the domestic dog (Canis familiaris) and in the grey fox (Urocyon cineroargenteus) have been examined. The dog satellite monomer is 737 bp long and contains 51% G + C; the grey fox satellite monomer is 880 b long and contains 54% G + C. The two satellites share three regions of 78, 92 and 314 bp with 70-80% sequence similarity. Sequence data from 16 monomers of dog satellite and 19 monomers of grey fox satellite demonstrate that the substitution spectra are different in the two canid species. For example, substitutions involving G or C residues are much more common in the grey fox satellite than in the domestic dog satellite despite their similar G + C contents.

Satellite DNA sequences in the neotropical marmoset Callimico goeldii (Primates, Platyrrhini)

Two families of tandemly repeated satellite DNAs were isolated from the neotropical primate Callimico goeldii (Goeldi's marmoset). One satellite, CgoA, is over 70% A + T and has a monomer length of 338 bp. The other satellite, CgoB, is 50% A + T and has a monomer length of 916 bp. Both CgoA and CgoB hybridize strongly with Callimico DNA, but not with the DNA of other new and old world primates. Based upon a neutral substitution rate of 1.5 X 10(-9)/site per year for primates, sequence data from 15 CgoA monomers indicate that the tandem array is at least 30 million years old. Since no other neotropical primate has amplified CgoA sequences, the data suggest that the ancestor of Callimico separated from the other neotropical primates at least 30 million years ago. This value is about fourfold larger than the value of 7-9 million years derived from immunological data by Sarich and Cronin (1980). Possible reasons for this discrepancy are discussed.

Subfamily structure and evolution of the human L1 family of repetitive sequences

Comparative analysis of the available 3'-portions of the human L1 (LINE-1) family of repeated sequences indicates that all the sequences can be classified in two major subfamilies. The division is based on patterns of diagnostic bases shared within L1 subfamilies of sequences but differing between them. The overall ratio of replacement to synonymous positions, occupied by the diagnostic bases in the large open reading frame of the L1 sequence, is 1.15. This indicates that both subfamilies were obtained from genes coding for functional proteins. The L1 subfamilies appear to be of different ages and may represent a "fossil record" of the same active gene at different times in the history of primates. The younger subfamily can be split further into at least two closely related branches of sequences. The above facts combined with the recent data for the Alu subfamily structure show that LINE and SINE families of interspersed repeats share discontinuous patterns in their evolution. These data are consistent with the model that both Alu and L1 families, as well as other pseudogene families, contain active genes producing discrete layers of pseudogenes throughout the history of primates. Models of evolutionary processes that could generate these discontinuities are discussed together with the possible biological role of Alu and L1 genes.

Chromosomal recombination and breakage associated with instability in mouse centrometric satellite DNA

A mouse L cell line containing the centromeric insertion of herpes thymidine kinase genes (tk) was previously shown to undergo a high frequency of DNA rearrangement at the site of tk insertion. Analysis of TK- revertants had demonstrated that DNA rearrangements were usually associated with DNA deletion and were always mediated by intrachromosomal recombinations. In this study, we further analyzed several TK+ subclones to examine the mode of DNA rearrangements in the absence of negative selection pressure. In two clones, LC2-3F and LC2-3E17, rearrangements were accompanied by DNA amplification and were mediated by intrachromosomal recombination. In subclone LC2-3E17-19, we further detected perturbations in the pattern of centromeric heterochromatization. This was associated with chromosome instability, as evidenced by chromosome breakage at the centromere. The analysis of three other sibling clones, LC2-3, LC2-6 and LC2-15, further suggests that reciprocal recombination events may play a role in such centromeric rearrangements. These results suggest that DNA rearrangements in the centromere may be mediated by a number of different mechanisms, and generally do not affect chromosome stability except when accompanied by changes in the pattern of heterochromatization.

Sequence-directed curvature of repetitive AluI DNA in constitutive heterochromatin of Artemia franciscana

An Alu I family of repeated DNA sequence 113 bp in length was found to be the major component of the heterochromatin in Artemia franciscana. On the basis of the analysis of cloned oligomeric (monomer to examer) heterchromatic fragments we predicted that the sequence could produce a stable curvature in chromosomal DNA. This prediction was confirmed by polyacrylamide gel electrophoresis analysis and by electron microscope observations. The anomalous mobility of these fragments is reversed when the DNA samples are electrophoresed in the presence of distamycin A. Moreover treatment of living Artemia with this drug produces visible decondensation of heterochromatic masses in the interphase nuclei.

Oligonucleotide-priming methods for the chromosome-specific labelling of alpha satellite DNA in situ

It is demonstrated that either general staining of the centromeric regions of all primate chromosomes, or selective staining of the centromeric region of specific chromosomes, may be obtained in preparations of metaphase chromosomes by probing specifically for different regions within the alpha satellite DNA monomer. In order to exploit observed patterns of sequence variation within the monomer for this purpose, we have developed two new DNA analysis methods. In PRimed IN Situ labelling (PRINS), synthetic oligonucleotides derived from subsections of the monomer are hybridized to the chromosomes. The oligonucleotides then serve as primers for the in situ incorporation of biotin-labelled nucleotides catalysed by Klenow polymerase. Incorporated biotin is visualized with fluorescein isothiocyanate-labelled avidin (FITC-avidin). In Primed Amplification Labelling (PAL), biotin-labelled hybridization probes are produced in a polymerase chain reaction (PCR, Saiki et al. 1985), in which two synthetic oligonucleotide primers anneal within the same monomer. With the right choice of primers libraries of labelled probes derived from most monomers present as templates are produced. If DNA from a specific chromosome is used as template, then the resulting probe mixture gives stronger and more chromosome-specific signals in in situ hybridization experiments than does a cloned alpha satellite DNA probe derived from the same chromosome. The results obtained indicate that the alpha-repeat monomer is composed of regions with different degrees of chromosome specificity.

Mouse major (gamma) satellite DNA is highly conserved and organized into extremely long tandem arrays: implications for recombination between nonhomologous chromosomes

We have isolated and sequenced 30 independent clones derived from MnlI digestion of purified mouse major (gamma) satellite DNA. These clones contained between 0.9 and 1.1 gamma monomeric units derived presumably from random chromosomal sources. Individual clones showed a mean deviation from the mouse consensus satellite sequence of 3.9%, with a range of 0.9-9.1%. Cleavage of total mouse LTK cell genomic DNA with three different restriction enzymes (HindIII, BglII, BamHI) that do not cut within satellite monomers, followed by Southern and pulsed-field gel electrophoretic analyses, showed that the majority of monomers were organized into largely uninterrupted arrays that varied from a minimum of 240 kb to greater than 2000 kb in length. We suggest that the high degree of conservation of the mouse gamma-satellite sequences throughout the mouse genome results from frequent recombinational exchange between nonhomologous chromosomes. Further, this same process, facilitated by the all-acrocentric constitution of the typical mouse karyotype, and the extremely long and homologous gamma-satellite arrays, may be related to the common occurrence of Robertsonian translocation in mouse.

Isolation of a novel mildly repetitive DNA sequence that is predominantly located at the terminus of the short arm of chromosome 4 near the Huntington disease gene

A novel mildly repetitive DNA sequence that is reiterated approximately 20 times in the human genome has been isolated and characterized. Most of the repeat units are localized very near the terminus of the short arm of chromosome 4 (4p) in the region known to contain the Huntington disease (HD) gene. A cloned probe that detects the repeated sequence reveals a restriction fragment length polymorphism that is close to and/or distal to the most distal genetic locus on 4p. This probe, therefore, provides a new genetic marker very close to and possibly flanking the HD gene. In addition, this probe should prove very useful for detailed physical mapping of the most distal region of 4p around the HD gene. The few (two or three) copies of this repeat not located near the terminus of 4p are located near the ends of two other chromosomes, 14 and 21.

A review of mitosis in the fission yeast Schizosaccharomyces pombe

Mitosis and cell division are the final events of the cell cycle, resulting in the precise segregation of chromosomes into two daughter cells. A highly controlled and accurate segregation of the chromosomes is required to ensure that each daughter cell receives a complete genome and remains viable. The fission yeast, Schizosaccharomyces pombe, is a unicellular eukaryotic organism which is particularly convenient for investigating these problems. It is very amenable to genetic analysis and its predominantly haploid life cycle has allowed the isolation of recessive temperature-sensitive mutants unable to complete the cell cycle. Classical genetic analysis of these mutants has been used to identify over 40 gene functions that are required for cell cycle progress in S. pombe. Many of these genes have now been cloned and sequenced and in some cases the encoded gene product has been identified. This approach, coupling classical and molecular genetics, allows identification of the molecules important in the mitotic processes and provides a means for establishing what functional roles they may play.

DNA tertiary structures formed in vitro by misaligned hybridization of multiple tandem repeat sequences

DNA tertiary structures are shown to be formed by denaturation and reannealing in vitro of molecularly-cloned DNA containing multiple tandem repeat sequences. Electron microscopy of homoduplex DNA molecules containing the human c-Harvey-ras gene revealed knot-like structures which mapped to the position of the 812 bp variable tandem repeat (VTR) sequence. We propose that the structures result from slipped-strand mispairing within the VTR and hybridisation of homologous repetitive sequences in the single-stranded loops so produced. Similar structures were also found in freshly-linearized supercoiled plasmids. More complex knot-like structures were found in homoduplexes of a 4 kb tandem array from the hypervariable region 3' to the human alpha-globin locus. Formation of such DNA tertiary structures in vitro also provides a practical method for identifying and mapping direct tandem repeat arrays that are at least 800 bp long.

G-repeats: a novel hamster sine family

A fragment of a hamster repetitive element inserted into the aprt locus of a radiation-induced mutant is a member of a novel interspersed repetitive (SINE) family constituting approximately 0.3 to 0.5% of the hamster genome (30 to 50,000 family members). Since this family was first detected in a gene rearranged after exposure to gamma irradiation, we have called these G-repeats. In common with other repetitive elements, members of this family are about 300 bp in length, are highly divergent (an average of 30% from the consensus), have an A + T rich sequence flanking one side, and can be found in short polydisperse circular (SPC) DNA. In contrast to some other families, G-repeats are not flanked by short direct repeats and lack sequences corresponding to the RNA polymerase III consensus promoter.

Molecular characterization of human minichromosomes with centromere from chromosome 1 in human-hamster hybrid cells

In this study we examine the amounts of four different human satellite DNA sequences in a series of human-hamster hybrid cells, which contain a human minichromosome including the centromere of human chromosome 1. Comparisons with the corresponding amounts in an intact human chromosome 1 suggest that the minichromosomes have lost satellite DNA sequences, and in one case a substantial fraction of several satellite DNAs is lost, without affecting the stability and normal mitotic segregation of the minichromosome. The smallest minichromosome appears to have lost all of the long arm and a significant portion of centromeric heterochromatin, while retaining 1000-2000 kb of the short arm of human chromosome 1. The satellite sequences examined include: a chromosome 1-specific satellite III probe, a chromosome 1-specific alpha satellite DNA, another alpha satellite DNA originally derived from the X chromosome, and an alphoid EcoRI dimer whose isolation from one of the minichromosomes and characterization is also described in this paper. One interpretation of these data indicates that an interspersion of blocks of satellite sequences occurs in the centromere region of chromosome 1. If these satellite sequences have functional significance, then there may be redundancy in the system that allows for a variation in the size of the kinetochore and the number of attachment sites for microtubules.

Occurrence of the (GATA)n sequences in vertebrate and invertebrate genomes

Clusters of the tetranucleotide GATA are found throughout the mouse genome with a major concentration on the Y chromosome. In Drosophila melanogaster, by contrast, they have a significant concentration on the X chromosome. Largely on the basis of these sex chromosomal concentrations and on their transcriptional activity in the mouse, these simple sequence tracts have been thought to be important in sex-determining and X inactivation mechanisms in both vertebrates and invertebrates. In every tested case the interpretations of the data have been difficult and sometimes the data themselves have been conflicting. We demonstrate in this paper that significant tracts of (GATA)n are totally absent from ovine and bovine genomes and point out that none of the major clusters of these repetitive sequences are near any of the sex-determining genes in D. melanogaster. We conclude therefore that (GATA)n sequences are not conserved over long evolutionary time periods as has previously been thought. Their absence from at least two mammalian genomes places severe constraints on their possible functions.

Asymmetry in chromosome pairing: a major factor in de novo mutation and the production of genetic disease in man

At the outset of the meiotic pairing process in man, trial and error mismatching and misalignment, both within homologous pairs and between heterologues, can be observed cytologically. Pairing starts at early zygotene principally within subtelomeric regions where the synaptonemal complex initiates. In the present paper, evidence for the primary role in synaptic initiation of a GC rich minisatellite in the human XY pseudoautosomal segment is presented, and circumstantial evidence is provided to support the view that GC rich sequences (minisatellites and Alu repeats) function to promote pairing within autosomes. The known sequence hypervariability of proterminal human minisatellites, it is suggested, arises as a secondary consequence of unequal exchange after misalignment between tandem repeats at the outset of the pairing process. Unequal exchange within misaligned repeat sequences at early prophase of meiosis could make a major contribution to de novo germinal mutation (conversion, duplication, deficiency, inversion, translocation), with serious consequences in man for the production of hereditary disease. For somatic tissues, rare mispairing between G rich repeats followed by unequal exchange could be a key step in cancer progression. It might also explain somatic mosaicism in some non-neoplastic clinical conditions.

A LINE 1 sequence interrupts the rat alpha 2u globulin gene

The rat alpha 2u globulin gene family is composed of about 25 members with closely related structure. Several of these genes are transcriptionally active in the liver of adult males. We isolated about 50 independent genomic clones from the library and determined complete nucleotide sequences of two. Although they were alike and revealed structural features prerequisite for active genes, one cloned gene was interrupted in the 6th intron with about 900 bp 5' truncated and 3'-terminal triplicated form of LINE 1 sequence flanked by 16 bp complete direct repeat originating from the 6th intron. Within the inserted LINE 1 an excellent splicing acceptor homologue with a precedent lariat junction motif and multiple polyadenylation signals was identified. Thus, the possible production of a chimeric RNA, the last exon of which would be replaced by a part of LINE 1, has to be considered.

Identification of new human repetitive sequences: characterization of the corresponding cDNAs and their expression in embryonal carcinoma cells

We have identified new repeated interspersed DNA sequences by analysis of homologous RNA transcripts from a human teratocarcinoma cell line (NTERA-2 clone D1). The abundance of transcripts varies upon retinoic acid induced differentiation of NTERA-2/D1 cells, and it is highest when the cells display the embryonal carcinoma phenotype. The expression of these novel repeated sequences appears to be tissue specific as no detectable expression was found in various cell lines of different embryological derivation. Characterization of the RNA transcripts by analysis of recombinant cDNA clones indicated that transcripts of different genomic units are present in undifferentiated embryonal teratocarcinoma cells. Nucleotide sequencing of the cloned cDNAs reveals a complex structure composed by unique and tandemly repeated sub-elements.

Genome-specific repetitive sequences in the genus Oryza

Repetitive DNA sequences are useful molecular markers for studying plant genome evolution and species divergence. In this paper, we report the isolation and characterization of four genome-type specific repetitive DNA sequences in the genus Oryza. Sequences specific to the AA, CC, EE or FF genome types are described. These genome-type specific repetitive sequences will be useful in classifying unknown species of wild or domestic rice, and in studying genome evolution at the molecular level. Using an AA genome-specific repetitive DNA sequence (pOs48) as a hybridization probe, considerable differences in its copy number were found among different varieties of Asian-cultivated rice (O. sativa) and other related species within the AA genome type. Thus, the relationship among some of the members of AA genome type can be deduced based on the degree of DNA sequence similarity of this repetitive sequence.

Detection and molecular cloning of highly repeated DNA in the sea cucumber sperm

A highly reiterated sequence in the sperm DNA of the echinoderm Holothuria tubulosa has been isolated by digestion with EcoRI, and cloned in the phagemid Bluescript. The monomeric unit has a repeat length of 391 bp and is arranged in tandem. The uncloned genomic monomer as well as two independent cloned fragments have been sequenced. The repeated element constitutes about 1.8% of total Holothuria DNA which corresponds to a repetition frequency of about 1.4 x 10(5) copies per haploid complement. The repetitive sequence has a high A + T content (66.8%) characterized by scattered tracts of A and T residues with no apparent internal sub-repeats, although several inverted and direct repeats are present. Heterogeneity between monomers derived from individual clones is low, whereas sequence similarity to known repetitive elements appears to be negligible.

Distribution and sequence homogeneity of an abundant satellite DNA in the beetle, Tenebrio molitor

The mealworm beetle, Tenebrio molitor, contains an unusually abundant and homogeneous satellite DNA which constitutes up to 60% of its genome. The satellite DNA is shown to be present in all of the chromosomes by in situ hybridization. 18 dimers of the repeat unit were cloned and sequenced. The consensus sequence is 142 nt long and lacks any internal repeat structure. Monomers of the sequence are very similar, showing on average a 2% divergence from the calculated consensus. Variant nucleotides are scattered randomly throughout the sequence although some variants are more common than others. Neighboring repeat units are no more alike than randomly chosen ones. The results suggest that some mechanism, perhaps gene conversion, is acting to maintain the homogeneity of the satellite DNA despite its abundance and distribution on all of the chromosomes.

Nucleotide sequence, genomic organization and evolution of a major repetitive DNA family in tilapia (Oreochromis mossambicus/hornorum)

A highly repetitive DNA sequence from tilapia (Oreochromis mossambicus/hornorum) has been cloned and sequenced. It is a tandemly arrayed sequence of 237 bp and constitutes 7% of the fish genome. The copy number of the repeat is approximately 3 x 10(5) per haploid genome. DNA sequence analysis of 7 cloned repeats revealed a high degree of conservation of the monomeric unit. Within the monomeric unit, a 9 bp AT rich motif is regularly spaced approximately 30 bp apart and may represent the progenitor of the amplified sequence. One cloned repeat, Ti-14, contained a 30 bp deletion at a position flanked by a 7 bp direct repeat. The Ti-14 sequence appears to have been amplified independently of the major 237 bp tandem array. A higher-order repeat unit, defined by longer-range periodicities revealed by restriction endonuclease digestion, is further imposed on the tandem array.

Cytoplasmic localization of human repetitive DNA revealed by in situ hybridization

Previously, we showed that a human repetitive DNA sequence (Sau3A family) belonging to a satellite DNA is unstable and constantly excised from the chromosomes (R. Kiyama, H. Matsui, and M. Oishi, 1986, Proc. Natl. Acad. Sci. USA 83, 4665). The unusual property of the repetitive DNA, along with another repetitive DNA (Alu sequence), was further investigated by in situ hybridization in several different human cells including HeLa, bone marrow, and peripheral blood cells. We found that the excised repetitive DNA sequences are localized not only in nuclei, but also in cytoplasm. These results have confirmed the instability of these DNA sequences in the chromosomes and further suggest that the alpha satellite DNA and the Alu sequence which were excised from the chromosomes are released from nuclei to cytoplasm.

The multiple codes of nucleotide sequences

Nucleotide sequences carry genetic information of many different kinds, not just instructions for protein synthesis (triplet code). Several codes of nucleotide sequences are discussed including: (1) the translation framing code, responsible for correct triplet counting by the ribosome during protein synthesis; (2) the chromatin code, which provides instructions on appropriate placement of nucleosomes along the DNA molecules and their spatial arrangement; (3) a putative loop code for single-stranded RNA-protein interactions. The codes are degenerate and corresponding messages are not only interspersed but actually overlap, so that some nucleotides belong to several messages simultaneously. Tandemly repeated sequences frequently considered as functionless "junk" are found to be grouped into certain classes of repeat unit lengths. This indicates some functional involvement of these sequences. A hypothesis is formulated according to which the tandem repeats are given the role of weak enhancer-silencers that modulate, in a copy number-dependent way, the expression of proximal genes. Fast amplification and elimination of the repeats provides an attractive mechanism of species adaptation to a rapidly changing environment.

Chromosome specificity of satellite DNAs: short- and long-range organization of a diverged dimeric subset of human alpha satellite from chromosome 3

The human alpha satellite DNA family, like many highly repeated satellite DNAs in eukaryotic genomes, is organized in distinct chromosome-specific subsets. As part of investigations into the molecular and evolutionary basis for the chromosome-specific nature of such subsets, we report the isolation and characterization of alpha satellite sequences specific for human chromosome 3. This subset is characterized by a predominant tandemly arranged approximately 2.9 kb higher-order repeat unit which, in turn, consists of 17 tandem diverged monomer repeat units of approximately 171 bp. Nucleotide sequence analysis reveals that the chromosome 3 higher-order repeat units are comprised, at least in part, of diverged dimeric (approximately 340 bp) sub-repeats and that this divergence accounts for the chromosome-specific behavior of this subset. Pulsed-field gel electrophoresis demonstrates that the chromosome 3 higher-order repeat units are localized in large domains, at least 1000 kb in length. Familial restriction fragment length polymorphisms associated with the satellite subset can be detected by pulsed-field gel electrophoresis and may facilitate molecular analysis of interchromosomal variation.

Definition of a second dimeric subfamily of human alpha satellite DNA

We describe a new human subfamily of alpha satellite DNA. The restriction endonuclease XbaI cleaves this subfamily into a collection of fragments which are heterogeneous with respect to size. We compared the sequences of 6 clones from four different XbaI size classes. Clones from a single size class were not necessarily more related than clones from different classes. Clones from different size classes were found to produce almost identical hybridization patterns with XbaI-digested human genomic DNA. All clones were found to share a common dimeric repeat organization, with dimers exhibiting about 84% sequence identities, indicating that the clones evolved from a common progenitor alphoid dimer. We show that this subfamily, and the EcoRI dimer subfamily originally described by Wu and Manuelidis, evolved from different progenitor alphoid dimers, and therefore represent distinct human alphoid subfamilies.

The distribution of interspersed repetitive DNA sequences in the human genome

The distribution of interspersed repetitive DNA sequences in the human genome has been investigated, using a combination of biochemical, cytological, computational, and recombinant DNA approaches. "Low-resolution" biochemical experiments indicate that the general distribution of repetitive sequences in human DNA can be adequately described by models that assume a random spacing, with an average distance of 3 kb. A detailed "high-resolution" map of the repetitive sequence organization along 400 kb of cloned human DNA, including 150 kb of DNA fragments isolated for this study, is consistent with this general distribution pattern. However, a higher frequency of spacing distances greater than 9.5 kb was observed in this genomic DNA sample. While the overall repetitive sequence distribution is best described by models that assume a random distribution, an analysis of the distribution of Alu repetitive sequences appearing in the GenBank sequence database indicates that there are local domains with varying Alu placement densities. In situ hybridization to human metaphase chromosomes indicates that local density domains for Alu placement can be observed cytologically. Centric heterochromatin regions, in particular, are at least 50-fold underrepresented in Alu sequences. The observed distribution for repetitive sequences in human DNA is the expected result for sequences that transpose throughout the genome, with local regions of "preference" or "exclusion" for integration.

Chromosome instability associated with human alphoid DNA transfected into the Chinese hamster genome

Repetitive DNA sequences have been implicated in the mediation of DNA rearrangement in mammalian cells. We have tested this hypothesis by using a dihydrofolate reductase (DHFR) expression vector into which candidate sequences were inserted. DHFR- Chinese hamster ovary (CHO) cells were transfected with this vector, the amplification of which was then selected for by methotrexate (MTX) exposure. Cells transfected with the vector alone (and resistant to 0.02 or 1.0 microM MTX) or with a poly(dG-dT) insert (and resistant to 0.05 or 1.0 microM MTX) showed little change in chromosome aberrations or sister chromatid exchange frequencies. In contrast, transfection of DHFR- CHO cells with a vector containing either of two distinct 0.34-kilobase human alphoid DNA segments (and selection to 0.05 to 10.0 microM MTX) showed an approximately 50% increase in chromosome number and marked changes in chromosome structure, including one or two dicentric or ring forms per cell. The sister chromatid exchange frequency also increased, to more than double the frequency of that in cells transfected without insert or those containing poly(dG-dT). In situ hybridization of one 0.34-kilobase insert in some cells suggested clustering of homologous sequences in structurally abnormal recipient CHO cell chromosomes. The approach described provides an introduction to a unique means for a coordinate molecular and cytological study of dynamic changes in chromosome structure.

Macromolecular organization of human centromeric regions reveals high-frequency, polymorphic macro DNA repeats

To analyze the macromolecular organization of human centromeric regions, we used alpha-satellite, or alphoid, repetitive DNA sequences specific to the centromeres of human chromosomes 6 (D6Z1), X (XC), and Y (YC-2) and the technique of pulsed-field gel electrophoresis. Genomic DNA from 24 normal, unrelated individuals was digested and separated into fragments ranging from 23 kilobases (kb) to 2 megabases (Mb) in length. Digestion with 12 different restriction enzymes with 4- to 8-base-pair recognition sequences and hybridization with alphoid sequences revealed chromosome-specific hybridization patterns. Similarities in the organization of the centromeric regions of the three chromosomes included NotI, SfiI, and SalI fragments of greater than 2 Mb and Sau3A1 and Alu I fragments of less than 150 kb. Each restriction enzyme with a 6-base-pair recognition sequence (Ava II, BamHI, HindIII, Hpa I, Pst I, Sal I, Sst I, and Xba I) detected polymorphic DNA fragments of 50 kb to 2 Mb. Forty percent or more of the individuals screened revealed a unique hybridization pattern with these enzymes and at least one of the three chromosome-specific alphoid probes. Five individuals differed from one another in hybridization pattern for each of the three enzymes HindIII, HpaI, and SstI and for each of the three centromeric probes. All 24 individuals could be distinguished on the basis of unique hybridization patterns with only two enzymes and one chromosome-specific alphoid probe. Family studies showed that these polymorphisms are inherited. The high frequency of these macro restriction fragment length polymorphisms illustrates the high degree of variability of the centromeric region among normal individuals and demonstrates its usefulness for DNA fingerprinting and pericentromeric mapping by linkage analysis.

Use of human alpha-satellite deoxyribonucleic acid to detect Y-specific centromeric sequences

The Y alphoid deoxyribonucleic acid probe Y97 has proved to be specific for the human Y centromere and to define a Y-specific 5.5 kb Eco RI fragment. Three experiments were designed to evaluate the sensitivity and the specificity of this Y alphoid probe Y97. In the first experiment the centromeric Y-specific 5.5 kb Eco RI fragment was clearly seen in the mixture of 0.050 microgram of male DNA with 4.950 micrograms of female DNA (1%). In the second experiment the same dilutional study was applied to the Yq11-related probe 4B-2 for comparison purpose. In the third experiment, hybridization with the Y97 probe was performed on 20 subjects with mosaic cell lines containing a cytogenetically identifiable Y (n = 10) and a cytogenetically unidentifiable minute (n = 10) fragment. Nineteen of the 20 subjects demonstrated the Y-specific 5.5 kb Eco RI hybridization band with the centromeric Y97 probe. These experiments demonstrated the utility of the Y97 probe to consistently identify cytogenetically altered Y chromosome fragments and confirm the mapping of the alphoid repeat sequences to the centromeric region of the Y chromosome.

Screening of Israeli Holstein-Friesian cattle for restriction fragment length polymorphisms using homologous and heterologous deoxyribonucleic acid probes

Genomic DNA of Israeli Holstein-Friesian dairy cattle were screened with a battery of 17 cloned or subcloned DNA probes in an attempt to document restriction fragment length polymorphisms at a number of genetic loci. Restriction fragment length polymorphisms were observed at the chymosin, oxytocin-neurophysin I, lutropin beta, keratin III, keratin VI, keratin VII, prolactin, and dihydrofolate reductase loci. Use of certain genomic DNA fragments as probes produced hybridization patterns indicative of satellite DNA at the respective loci. Means for distinguishing hybridizations to coding sequences for unique genes from those to satellite DNA were developed. Results of this study are discussed in terms of strategy for the systematic development of large numbers of bovine genomic polymorphisms.

Nucleotide sequence and transcription of a rat tRNA(Phe) gene and a neighboring Alu-like element

A bacteriophage gamma Ch4A clone containing a 22-kb rat DNA insert was isolated and found to contain a solitary tRNA(Phe)GAA gene and, 436 bp downstream of it, an Alu-like element. The nucleotide sequence of a 1141-bp DNA fragment containing these genes was determined. The rat tRNA(Phe)GAA gene, with the exception of an additional A in the extra arm, has a sequence identical to that of a rabbit liver tRNA(Phe). The Alu-like element belongs to the rodent B2 family of short interspersed repetitive nucleotide sequences. This repetitive element, B2Phe, is flanked by 12-bp direct repeats, contains an internal split promoter (block A and block B) for RNA polymerase III and is devoid of an A-rich segment at the 3' end. Like other members of the B2 family, the B2Phe element presents 64% sequence homology with rat serine tRNA and contains a serine (GCT) anticodon. Both tRNA(Phe)GAA gene and B2Phe element were found to be transcriptionally active in HeLa cell and Xenopus oocyte nuclear extracts. The tRNA(Phe) gene transcripts were processed during the course of transcription to form mature-size tRNA(Phe). The transcription efficiency of the B2Phe element was found to be an order of magnitude higher than that of the tRNA(Phe) gene. Competition experiments demonstrate that the B2Phe DNA can form a more stable transcription complex than the tRNA(Phe) gene and compete with it for binding of transcription factors.

A new family of repetitive, retroposon-like sequences in the genome of the rainbow trout

We have identified a new family of interspersed, moderately repetitive DNA elements, termed the RSg-1 family, in the genome of the rainbow trout. Two of the elements examined here are situated upstream of sequences which code for trout nuclear proteins; a protamine gene (p101) and the clustered histone H4 gene. Sequence comparison of various RSg-1 elements indicated a high degree of nucleotide sequence homology between different members of the family. These repetitive elements exhibit well defined 3' ends which contain poly(A) segments preceded by the consensus polyadenylation signal AATAAA. Sequences flanking the 3' end of the poly(A) tract also conform to a consensus sequence. A similar sequence is also found flanking the 5' terminus of the element in the protamine clone p101, and thus may represent a target-site duplication generated upon insertion of the element into the genome. These characteristics, together with the heterogeneous nature of the 5' ends of the elements, are reminiscent of processed pseudogenes and retroposons such as the mammalian L1 family of interspersed repetitive elements.

A highly conserved repetitive DNA sequence, (TTAGGG)n, present at the telomeres of human chromosomes

A highly conserved repetitive DNA sequence, (TTAGGG)n, has been isolated from a human recombinant repetitive DNA library. Quantitative hybridization to chromosomes sorted by flow cytometry indicates that comparable amounts of this sequence are present on each human chromosome. Both fluorescent in situ hybridization and BAL-31 nuclease digestion experiments reveal major clusters of this sequence at the telomeres of all human chromosomes. The evolutionary conservation of this DNA sequence, its terminal chromosomal location in a variety of higher eukaryotes (regardless of chromosome number or chromosome length), and its similarity to functional telomeres isolated from lower eukaryotes suggest that this sequence is a functional human telomere.

Localisation of satellite DNA sequences on human metaphase chromosomes using bromodeoxyuridine-labelled probes

Human highly repeated satellite sequences, cloned into M13, were used as templates to prepare single-stranded DNA probes containing bromodeoxyuridine (BrdUrd) in place of thymine. The probes were hybridised to human metaphase chromosomes and visualised using an indirect immunological detection procedure. The sensitivity and accuracy of the technique were tested using a BrdUrd-labelled probe of known copy number and location: a segment from the 2.5 kb Y chromosome repeat. The procedure proved to be reliable and fast, with a sensitivity similar to that of other in situ hybridisation techniques. The technique was then used to determine the chromosomal locations of a 100 bp repeat from human satellite 3. The satellite 3 probe hybridised to a large number of chromosomes and, surprisingly, the intensity of label at all locations remained unchanged when the slides were washed at a higher stringency. The resolution of the technique was very high and allowed accurate localisation of the satellite sequence. Hybridisation was observed in two regions of the subcentromeric heterochromatin of chromosome 9, in two locations at the centromere and short arm of all the acrocentric autosomes, and at the centromere and long arm of the Y chromosome. In addition the probe hybridised to centromeric heterochromatin in chromosomes 1, 16, 17 and 20. We believe that single-stranded BrdUrd-labelled probes should be very useful for detecting RNA transcripts in cells, and discuss ways by which the procedure could be modified to locate single copy DNA on chromosomes.

Chromosome instability associated with human alphoid DNA transfected into the Chinese hamster genome

Repetitive DNA sequences have been implicated in the mediation of DNA rearrangement in mammalian cells. We have tested this hypothesis by using a dihydrofolate reductase (DHFR) expression vector into which candidate sequences were inserted. DHFR- Chinese hamster ovary (CHO) cells were transfected with this vector, the amplification of which was then selected for by methotrexate (MTX) exposure. Cells transfected with the vector alone (and resistant to 0.02 or 1.0 microM MTX) or with a poly(dG-dT) insert (and resistant to 0.05 or 1.0 microM MTX) showed little change in chromosome aberrations or sister chromatid exchange frequencies. In contrast, transfection of DHFR- CHO cells with a vector containing either of two distinct 0.34-kilobase human alphoid DNA segments (and selection to 0.05 to 10.0 microM MTX) showed an approximately 50% increase in chromosome number and marked changes in chromosome structure, including one or two dicentric or ring forms per cell. The sister chromatid exchange frequency also increased, to more than double the frequency of that in cells transfected without insert or those containing poly(dG-dT). In situ hybridization of one 0.34-kilobase insert in some cells suggested clustering of homologous sequences in structurally abnormal recipient CHO cell chromosomes. The approach described provides an introduction to a unique means for a coordinate molecular and cytological study of dynamic changes in chromosome structure.

Characterization of highly repetitive sequences of Arabidopsis thaliana

We have analyzed three classes of highly repetitive DNA sequences of Arabidopsis thaliana, composed of tamdemly repeated units of 180 bp, 500 bp, and 160 bp, respectively. The three families comprise approximately 2% of the Arabidopsis genome and are the major component of the highly repetitive DNA. The 500-bp element arose by duplication of one half of a 180-bp ancestor and insertion of a foreign segment between the two duplicated parts followed by amplification. The repeat elements contain occasionally palindromes and other motifs but none are significantly conserved. There is no significant similarity with previously published repetitive elements. Heterogeneity between monomers ranges from 6% to 17%. Monomers derived from different clusters in the genome are more diverged than monomers of the same array.

Chromosome-specific alpha satellite DNA: isolation and mapping of a polymorphic alphoid repeat from human chromosome 10

Distinct subsets of the human alpha satellite repetitive DNA family can be found in the centromeric region of each chromosome. Here we described the isolation and mapping of an alpha satellite repeat unit specific for human chromosome 10, using a somatic cell hybrid in which the only human centromere derives from chromosome 10. A hierarchical higher-order repeat unit, consisting of eight tandem approximately 171-bp alphoid monomer units, is defined by six restriction endonucleases. Under high-stringency conditions, a cloned representative of this 8-mer repeat family hybridizes to chromosome 10 only, both by Southern blot analysis of a somatic cell hybrid panel and by in situ hybridization. The probe furthermore detects a polymorphic restriction pattern of the alpha satellite array on chromosome 10. These features will make this probe a valuable genetic marker for studies of the centromeric region of chromosome 10.

Human satellite-III DNA: an example of a "macrosatellite" polymorphism

Human satellite III DNA contains a complex polymorphism, which appears to be TaqI-specific. Its likely cause is a two-step point mutation in the pentameric repeat TTCCA, typical of satellite III. Hybridization of the satellite-III sequence-related probe that demonstrates this polymorphism is directly attributable to clusters of "pure" pentameric TTCCA repeats in the genome. The sites of such repeats include the 3.4-kb fragment specific to the Y chromosome and a limited number of autosomes. The polymorphism arises from the latter and is likely to include chromosomes containing so-called K domain satellite III sequences found, for example, in chromosomes 9 and 15. Segregation of the polymorphic fragments appears to follow orthodox genetics.

The phylogeny of human chromosome specific alpha satellites

The chromosomal distribution of sequences homologous to 18 coned alpha satellite fragments was established by in situ hybridization. It appeared that all the cloned sequences were members of small repeated families located on single chromosome pairs. Among the sequences studied specific molecular markers for chromosomes 3, 4, 10, 11, 17, 18 and X were found. Comparison of the hybridization spectra obtained under non-stringent conditions and of restriction site periodicities in different chromosome-specific families allowed the identification of three "suprachromosomal" families, each located on a characteristic set of chromosomes. The three families together cover all the autosomes and the X chromosome. These data plus those reported previously allow part of the phylogenetic tree of chromosome-specific alpha satellite repeats to be drawn. Each suprachromosomal family has presumably originated from a distinct ancestral sequence and consists of certain types of monomers. Ancestral sequences have evolved into a number of chromosome-specific families by cycles of interchromosomal transfers and subsequent amplification events. The high homogeneity of chromosome-specific families may be a result of intrachromosomal homogenization of amplification units in chromosome-specific alpha satellite domains.

In situ hybridization as a tool to study numerical chromosome aberrations in solid bladder tumors

Methods for single- and double-target in situ hybridization (ISH) to, cells isolated from solid transitional cell carcinomas (TCC's) of the urinary bladder are described. Single cell suspensions were prepared from solid tumors of the urinary bladder by mechanical disaggregation and fixed in 70% ethanol. Using two DNA probes specific for the centromeres of chromosomes #1 and #18, ISH procedures were optimized for these samples. Human lymphocytes and cells from the T24 bladder tumor cell line were used as controls. In lymphocyte nuclei and metaphase chromosome spreads, ISH showed two major spots for each of the probes. About 80% of the nuclei from T24 cells showed three spots for both the chromosome #1 and #18 specific probes. When nuclei from TCC's were analyzed, often the number of spots for chromosome #1, and to a lesser extent for chromosome #18, differed from the number expected on basis of flow cytometric ploidy measurements. The double target-ISH method in all cases allowed the correlation of numerical aberrations for chromosomes #1 and #18 in one and the same cell. By such analyses a profound heterogeneity in chromosome number was detected in most tumors. In order to optimize the reproducibility of the method and the interpretation of the ISH-signals, criteria for their analysis have been determined. This procedure can now be applied on a routine basis to solid tumor specimens.

Cloning of a major repeat DNA sequence from Pyura stolonifera

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

The human factor VII gene is polymorphic due to variation in repeat copy number in a minisatellite

The gene coding for human factor VII, a vitamin K-dependent coagulation factor, contains five minisatellite imperfect tandem repeats with monomer element lengths ranging from 14 to 37 bp, and copy numbers ranging from 6 to 52. Three of these repeats are entirely within introns, one is entirely in an untranslated portion of an exon, and one spans an exon-intron border and contains coding sequence. A consensus sequence derived from a comparison of the monomers is similar to a core sequence found in other minisatellites. All of the minisatellites display higher-order periodicities. At least one of these minisatellites is polymorphic. A variation in repeat copy number has been observed in a tandem-repeat region in the seventh factor-VII intron.

Close relationship between non-viral retroposons in Drosophila melanogaster

G elements constitute one of the several moderately repeated DNA families of the Drosophila melanogaster genome. G elements lack terminal repetitions and structurally resemble mammalian processed pseudogenes because they terminate at one end in oligo-A tracts of variable length. G elements are mostly interspersed in the chromocentric heterochromatin with other repeated DNA sequences. Nucleotide sequence analysis of G3A, a family member inserted in a non-nucleolar rDNA unit, shows that functional G elements might have coding capacity for two polypeptides; one has homology to reverse transcriptases, the other is reminiscent of RNA binding proteins derived from the cleavage of retroviral gag polyproteins. Functionally related polypeptides are similarly encoded by members of two other Drosophila repeated DNA families, the F elements and the I factors. The similarity in structural organization and the relatedness of their potential gene products favors the hypothesis that G, F, and I sequences derive from a common ancestor and result from processes based on the reverse transcription of RNA intermediates that probably differ markedly from those ensuring the maintenance and dispersion of copia-like elements.

Human genome organization: Alu, lines, and the molecular structure of metaphase chromosome bands

Combining high resolution in situ hybridization with quantitative solid state imaging, we show that human metaphase chromosome Giemsa/Quinacrine and Reverse bands are each characterized by distinct families of interspersed repeated sequences: the SINES, Alu family dominates in Reverse bands, and the LINES, L1 family dominates in Giemsa/Quinacrine positive bands. Alu is 56% guanine plus cytosine, and L1 is 58% adenine plus thymine, and each may comprise 13%-18% of the total DNA in a chromosome band. Therefore, the distribution of these sequences alone may account for a large part of human chromosome banding seen with fluorescent dyes. With the exception of some telomeric regions, and the chromosomal regions of simple sequence DNA, Alu and L1 are precisely inversely distributed, suggesting an inverse functional relationship. This finding links genome organization with chromosome structure and function.

Structural organization and functional analysis of centromeric DNA in the fission yeast Schizosaccharomyces pombe

Centromeric DNA in the fission yeast Schizosaccharomyces pombe was isolated by chromosome walking and by field inversion gel electrophoretic fractionation of large genomic DNA restriction fragments. The centromere regions of the three chromosomes were contained on three SalI fragments (120 kilobases [kb], chromosome III; 90 kb, chromosome II; and 50 kb, chromosome I). Each fragment contained several repetitive DNA sequences, including repeat K (6.4 kb), repeat L (6.0 kb), and repeat B, that occurred only in the three centromere regions. On chromosome II, these repeats were organized into a 35-kb inverted repeat that included one copy of K and L in each arm of the repeat. Site-directed integration of a plasmid containing the yeast LEU2 gene into K repeats at each of the centromeres or integration of an intact K repeat into a chromosome arm had no effect on mitotic or meiotic centromere function. The centromeric repeat sequences were not transcribed and possessed many of the properties of constitutive heterochromatin. Thus, S. pombe is an excellent model system for studies on the role of repetitive sequence elements in centromere function.

Association of high rate of recombination with amplification of dominant selectable gene in human cells

The human cell line LM205, transformed with the pLR309 plasmid, contains a stably integrated selectable gene marker (neo) without a transcriptional promoter. Spontaneous tandem duplication at the integration site relocates a Simian virus 40 transcriptional promoter to a position 5' to the neo gene at a rate of 5 x 10(-8) events/cell/generation, as measured by subsequent resistance of the cells to the toxic antibiotic G418. The heterogeneity in the site of recombination observed in various G418-resistant (G418-R) subclones indicates that the sequences involved have little or no homology. The rate of tandem duplication involving the neo gene was not affected by DNA-damaging agents or by inhibitors of DNA synthesis. Although these tandem duplications were relatively stable in most G418-R subclones, others underwent further amplification of the neo gene during cloning. In one such cell line, RS-4, subclones isolated without G418 demonstrated a high degree of heterogeneity in the neo gene copy number (2-20), indicating that amplification was associated with a high rate of homologous recombination. Because LM205 was the only clone out of the 30 original clones transformed with pLR309 that demonstrated spontaneous G418-R colonies, cell DNA sequences near the integrated neo gene may promote this recombination. Inclusion of this cell DNA in the initial tandem duplication might then explain the high rate of duplication and deletion observed in the region of the neo gene in the RS-4 subclone.

Chromosomal localization of Sau3A repetitive DNA revealed by in situ hybridization

The Sau3A DNA family consists of unique alphoid human repetitive DNA which is prone to be excised from the chromosomes and exhibits restriction fragment length polymorphism. We studied the chromosomal localization of the DNA by in situ hybridization using cultured normal human lymphocytes. Under standard hybridization conditions, the sequence hybridized with the centromeric regions of chromosomes 1, 2, 4, 11, 15, 17, 18, 19 and X, but under high stringency hybridization conditions, it hybridized with the centromeric regions of chromosomes 1, 17 and X, and particularly chromosome 11. Based on these results, we discuss the evolutionary relationship among the sequences of the Sau3A DNA family.