Organization of a repetitive human 1.8 kb KpnI sequence localized in the heterochromatin of chromosome 15

The Dynamic Structure and Rapid Evolution of Human Centromeric Satellite DNA

The complete sequence of a human genome provided our first comprehensive view of the organization of satellite DNA associated with heterochromatin. We review how our understanding of the genetic architecture and epigenetic properties of human centromeric DNA have advanced as a result. Preliminary studies of human and nonhuman ape centromeres reveal complex, saltatory mutational changes organized around distinct evolutionary layers. Pockets of regional hypomethylation within higher-order α-satellite DNA, termed centromere dip regions, appear to define the site of kinetochore attachment in all human chromosomes, although such epigenetic features can vary even within the same chromosome. Sequence resolution of satellite DNA is providing new insights into centromeric function with potential implications for improving our understanding of human biology and health.

A classical revival: Human satellite DNAs enter the genomics era

The classical human satellite DNAs, also referred to as human satellites 1, 2 and 3 (HSat1, HSat2, HSat3, or collectively HSat1-3), occur on most human chromosomes as large, pericentromeric tandem repeat arrays, which together constitute roughly 3% of the human genome (100 megabases, on average). Even though HSat1-3 were among the first human DNA sequences to be isolated and characterized at the dawn of molecular biology, they have remained almost entirely missing from the human genome reference assembly for 20 years, hindering studies of their sequence, regulation, and potential structural roles in the nucleus. Recently, the Telomere-to-Telomere Consortium produced the first truly complete assembly of a human genome, paving the way for new studies of HSat1-3 with modern genomic tools. This review provides an account of the history and current understanding of HSat1-3, with a view towards future studies of their evolution and roles in health and disease.

Presence of 15p Marker D15Z1 on the Short Arm of Acrocentric Chromosomes is Associated with Aneuploid Offspring in Mexican Couples

Variation in the location of the 15p region D15Z1 is recognized as a polymorphism in several human populations. We used high-stringency Fluorescence In Situ Hybridization (FISH) to detect D15Z1 in a Mexican cohort. Here, we report the presence of extra D15Z1 sequences on the p-arm of acrocentric chromosomes other than 15 in two groups of Mexican couples, one with healthy offspring (n = 75) and the other with aneuploid offspring (n = 87), mainly trisomy 21. The additional D15Z1 polymorphism was significantly increased in individuals with aneuploid offspring (26.4%), in comparison to individuals with healthy offspring (14%). The most frequent acceptor chromosome of D15Z1 was chromosome 13p, followed by 14p, and finally, 21p. Our results show an overall frequency of 21.6% of this polymorphism in the Mexican population and suggest that its presence might be associated with the mis-segregation of other acrocentric chromosomes and aneuploid offspring. The high frequency of the polymorphism of the D15Z1 sequence on acrocentric chromosomes other than 15 suggests a sequence homogenization of the acrocentric p arms, related to the important function of the centromere and the nucleolar organization region, which flank satellite III DNA.

Genomic characterization of large heterochromatic gaps in the human genome assembly

The largest gaps in the human genome assembly correspond to multi-megabase heterochromatic regions composed primarily of two related families of tandem repeats, Human Satellites 2 and 3 (HSat2,3). The abundance of repetitive DNA in these regions challenges standard mapping and assembly algorithms, and as a result, the sequence composition and potential biological functions of these regions remain largely unexplored. Furthermore, existing genomic tools designed to predict consensus-based descriptions of repeat families cannot be readily applied to complex satellite repeats such as HSat2,3, which lack a consistent repeat unit reference sequence. Here we present an alignment-free method to characterize complex satellites using whole-genome shotgun read datasets. Utilizing this approach, we classify HSat2,3 sequences into fourteen subfamilies and predict their chromosomal distributions, resulting in a comprehensive satellite reference database to further enable genomic studies of heterochromatic regions. We also identify 1.3 Mb of non-repetitive sequence interspersed with HSat2,3 across 17 unmapped assembly scaffolds, including eight annotated gene predictions. Finally, we apply our satellite reference database to high-throughput sequence data from 396 males to estimate array size variation of the predominant HSat3 array on the Y chromosome, confirming that satellite array sizes can vary between individuals over an order of magnitude (7 to 98 Mb) and further demonstrating that array sizes are distributed differently within distinct Y haplogroups. In summary, we present a novel framework for generating initial reference databases for unassembled genomic regions enriched with complex satellite DNA, and we further demonstrate the utility of these reference databases for studying patterns of sequence variation within human populations.

At least 5–10% of the human genome remains unassembled, unmapped, and poorly characterized. The reference assembly annotates these missing regions as multi-megabase heterochromatic gaps, found primarily near centromeres and on the short arms of the acrocentric chromosomes. This missing fraction of the genome consists predominantly of long arrays of near-identical tandem repeats called satellite DNA. Due to the repetitive nature of satellite DNA, sequence assembly algorithms cannot uniquely align overlapping sequence reads, and thus satellite-rich domains have been omitted from the reference assembly and from most genome-wide studies of variation and function. Existing methods for analyzing some satellite DNAs cannot be easily extended to a large portion of satellites whose repeat structures are complex and largely uncharacterized, such as Human Satellites 2 and 3 (HSat2,3). Here we characterize HSat2,3 using a novel approach that does not depend on having a well-defined repeat structure. By classifying genome-wide HSat2,3 sequences into subfamilies and localizing them to chromosomes, we have generated an initial HSat2,3 genomic reference, which serves as a critical foundation for future studies of variation and function in these regions. This approach should be generally applicable to other classes of satellite DNA, in both the human genome and other complex genomes.

Putative CENP-B paralogues are not present at mammalian centromeres

Although centromere protein B (CENP-B) is a highly conserved mammalian centromere protein, its function remains unknown. The presence of the protein is required to form artificial satellite DNA-based centromeres de novo, yet cenpb knockout mice are viable for multiple generations with no mitotic or meiotic defects, and the protein is not present at fully functional neocentromeres. Previous studies have suggested that the presence of functionally redundant paralogues of CENP-B may explain the lack of a phenotype in knockout mice, and the related Tigger-derived (TIGD) family of proteins has been implicated as the most likely candidate for such paralogues. Here, we describe an investigation of the centromere-binding properties of the three TIGD proteins most highly related to CENP-B through phylogenetic analysis through EGFP fusion studies and immunocytochemistry. Although two of the three proteins bound to human centromeres with low affinity when overexpressed as fusion proteins, the strongest candidate, TIGD3, demonstrated no native centromeric binding when using raised antibodies, either in human cells or in cenpb (-/-) mouse ES cells. We conclude that the existence of functional CENP-B paralogues is highly unlikely and that CENP-B acts alone at the centromere. Based on these data, we suggest a new, meiotic drive model of CENP-B action during centromere repositioning in evolution.

Tandemly repeated DNA families in the mouse genome

Background

Functional and morphological studies of tandem DNA repeats, that combine high portion of most genomes, are mostly limited due to the incomplete characterization of these genome elements. We report here a genome wide analysis of the large tandem repeats (TR) found in the mouse genome assemblies.

Results

Using a bioinformatics approach, we identified large TR with array size more than 3 kb in two mouse whole genome shotgun (WGS) assemblies. Large TR were classified based on sequence similarity, chromosome position, monomer length, array variability, and GC content; we identified four superfamilies, eight families, and 62 subfamilies - including 60 not previously described. 1) The superfamily of centromeric minor satellite is only found in the unassembled part of the reference genome. 2) The pericentromeric major satellite is the most abundant superfamily and reveals high order repeat structure. 3) Transposable elements related superfamily contains two families. 4) The superfamily of heterogeneous tandem repeats includes four families. One family is found only in the WGS, while two families represent tandem repeats with either single or multi locus location. Despite multi locus location, TRPC-21A-MM is placed into a separated family due to its abundance, strictly pericentromeric location, and resemblance to big human satellites.

To confirm our data, we next performed in situ hybridization with three repeats from distinct families. TRPC-21A-MM probe hybridized to chromosomes 3 and 17, multi locus TR-22A-MM probe hybridized to ten chromosomes, and single locus TR-54B-MM probe hybridized with the long loops that emerge from chromosome ends. In addition to in silico predicted several extra-chromosomes were positive for TR by in situ analysis, potentially indicating inaccurate genome assembly of the heterochromatic genome regions.

Conclusions

Chromosome-specific TR had been predicted for mouse but no reliable cytogenetic probes were available before. We report new analysis that identified in silico and confirmed in situ 3/17 chromosome-specific probe TRPC-21-MM. Thus, the new classification had proven to be useful tool for continuation of genome study, while annotated TR can be the valuable source of cytogenetic probes for chromosome recognition.

Human chromosome 1 satellite 3 DNA is decondensed, demethylated and transcribed in senescent cells and in A431 epithelial carcinoma cells

Constitutive heterochromatin mainly consists of different classes of satellite DNAs and is defined as a transcriptionally inactive chromatin that remains compact throughout the cell cycle. The aim of this work was to investigate the level of condensation, methylation and transcriptional status of centromeric (alphoid DNA) and pericentromeric satellites (human satellite 3, HS3) in tissues (lymphocytes, placenta cells) and in cultured primary (MRC5, VH-10, AT2Sp) and malignant (A431) cells. We found that alphoid DNA remained condensed and heavily methylated in all the cell types. The HS3 of chromosome 1 (HS3-1) but not of chromosome 9 (HS3-9) was strongly decondensed and demethylated in A431 cells. The same observation was made for aged embryonic lung (MRC5) and juvenile foreskin (VH-10) fibroblasts obtained at late passages (32(nd) and 23(rd), respectively). Decondensation was also found in ataxia telangiectasia AT2Sp fibroblasts at the 16(th) passage. One of the manifestations of the disease is premature aging. The level of HS3-1 decondensation was higher in aged primary fibroblasts as compared to A431. The HS3-1 extended into the territory of neighbouring chromosomes. An RT-PCR product was detected in A431 and senescent MRC5 fibroblasts using primers specific for HS3-1. The RNA was polyadenylated and transcribed from the reverse chain. Our results demonstrate the involvement of satellite DNA in associations between human chromosomes and intermingling of chromosome territories. The invading satellite DNA can undergo decondensation to a certain level. This process is accompanied by demethylation and transcription.

A wide-range, low-cost 150 bp ladder for sizing DNA fragments between 150 and 4500 bp

Agarose gel electrophoresis, a very routine procedure, requires molecular weight standards; these are usually manufactured from plasmid or viral DNA fragments, or more recently, from PCR products of defined sizes. We describe here the preparation of a molecular weight standard from a completely different DNA source - the uniquely organized genome of the beetle Tenebrio molitor. The standard can be used to accurately size DNAs between 150 and 4500 bp, a useful range of sizes for many agarose gel electrophoresis applications, including separation of PCR products and plasmid cloning targets. In addition, it is easy to prepare, inexpensive, and rivals the best of the commercial ladders.

Distribution of the D15Z1 copy number polymorphism

Using fluorescent in situ hybridization (FISH) with the probe p15 (D15Z1), we investigated the distribution of the polymorphic 15p signal which has been reported to occur on acrocentric chromosomes in addition to chromosome 15. The short arm of chromosome 15 has a characteristic signal pattern when hybridized with the FISH probe D15Z1. However, the D15Z1 signal can occasionally be seen on the short arm of other acrocentric chromosomes. We studied the distribution of the D15Z1 probe in 1657 patients consisting both of individuals with a normal karyotype and those with a variety of chromosome abnormalities involving the acrocentric chromosomes. Our results show that one in six individuals, regardless of their patient ascertainment category or karyotypic status, had one or more additional D15Z1 signals, and that there were no significant differences in the distribution of extra signals among the patient groups.

A DA/DAPI positive human 14p heteromorphism defined by fluorescence in-situ hybridisation using chromosome 15-specific probes D15Z1 (satellite III) and p-TRA-25 (alphoid)

We have investigated the use of the satellite III probe, D15Z1, as an alternative to DA/DAPI staining in the identification of chromosome 15-derived markers. The probe hybridises to the short arm of chromosome 15 under high stringency conditions. We have screened 100 randomly selected patients, by fluorescence in-situ hybridisation (FISH), using co-hybridisation experiments with D15Z1 and a whole chromosome library, pBS-15. 88 individuals showed the expected pattern of two D15Z1 signals on the p-arm of both homologues of chromosome 15, whereas 12 individuals showed an additional signal on a third acrocentric D-group chromosome. Sequential GTC banding and D15Z1 hybridisation revealed that in each case it was one homologue of chromosome 14 that was D15Z1 positive. This pattern always correlated with positive DA/DAPI staining. In contrast, the 15 centromere-specific alphoid probe, pTRA-25, gave the expected two signals on both homologues of chromosome 15 in every case. Thus, D15Z1 and DA/DAPI signals co-localize while pTRA-25 is 15 centromere-specific and should be applied for unequivocal identification of chromosome 15-derived markers in clinical studies. The chromosome 14 heteromorphism, as identified by D15Z1, and defined by pTRA-25, may have arisen by intrachromosomal amplification or interchromosomal exchange.

Aneuploidy of human testicular germ cell tumors is associated with amplification of centrosomes

Testicular germ cell tumors occur in three age groups. Seminomas and nonseminomas of adults, including mature teratomas, and the precursor carcinoma in situ (CIS) are aneuploid. This also holds true for yolk sac tumors of newborn and infants, while the mature teratomas of this age are diploid. In contrast, spermatocytic seminomas occurring in the elderly contain both diploid and polyploid cells. Aneuploidy has been associated with centrosome aberrations, sometimes related to overexpression of STK15. Aneuploidy of non-neoplastic germ cells has been demonstrated in the context of male infertility, a risk factor for the development of seminoma/nonseminoma. We investigated aneuploidy, centrosome aberrations and the role of STK15 in different types of testicular germ cell tumors as well as in normal and disturbed spermatogenesis. The aneuploid seminomas and nonseminomas tumors (including CIS) showed increased numbers of centrosomes, without STK15 amplification or overexpression. Four out of six infantile teratomas had normal centrosomes, the remaining two and an infantile yolk sac tumor showed a heterogeneous pattern of cells with normal or amplified centrosomes. Spermatocytic seminomas had two, four or eight centrosomes. Germ cells in seminiferous tubules with disturbed spermatogenesis shared both aneuploidy and centrosome abnormalities with seminomas/nonseminomas and showed a more intense STK15 staining than those with normal spermatogenesis and CIS. Therefore, aneuploidy of testicular germ cell tumors is associated with amplified centrosomes probably unrelated to STK15.

Non-random radial higher-order chromatin arrangements in nuclei of diploid human cells

A quantitative comparison of higher-order chromatin arrangements was performed in human cell types with three-dimensionally (3D) preserved, differently shaped nuclei. These cell types included flat-ellipsoid nuclei of diploid amniotic fluid cells and fibroblasts and spherical nuclei of B and T lymphocytes from peripheral human blood. Fluorescence in-situ hybridization (FISH) was performed with chromosome paint probes for large (#1-5) and small (#17-20) autosomes, and for the two sex chromosomes. Other probes delineated heterochromatin blocks of numerous larger and smaller human chromosomes. Shape differences correlated with distinct differences in higher order chromatin arrangements: in the spherically shaped lymphocyte nuclei we noted the preferential positioning of the small, gene dense #17, 19 and 20 chromosome territories (CTs) in the 3D nuclear interior--typically without any apparent connection to the nuclear envelope. In contrast, CTs of the gene-poor small chromosomes #18 and Y were apparently attached at the nuclear envelope. CTs of large chromosomes were also preferentially located towards the nuclear periphery. In the ellipsoid nuclei of amniotic fluid cells and fibroblasts, all tested CTs showed attachments to the upper and/or lower part of the nuclear envelope: CTs of small chromosomes, including #18 and Y, were located towards the centre of the nuclear projection (CNP), while the large chromosomes were positioned towards the 2D nuclear rim. In contrast to these highly reproducible radial arrangements, 2D distances measured between heterochromatin blocks of homologous and heterologous CTs were strikingly variable. These results as well as CT painting let us conclude that nuclear functions in the studied cell types may not require reproducible side-by-side arrangements of specific homologous or non-homologous CTs. 3D-modelling of statistical arrangements of 46 human CTs in spherical nuclei was performed under the assumption of a linear correlation between DNA content of each chromosome and its CT volume. In a set of modelled nuclei, we noted the preferential localization of smaller CTs towards the 3D periphery and of larger CTs towards the 3D centre. This distribution is in clear contrast to the experimentally observed distribution in lymphocyte nuclei. We conclude that presently unknown factors (other than topological constraints) may play a decisive role to enforce the different radial arrangements of large and small CTs observed in ellipsoid and spherical human cell nuclei.

Identification and characterization of satellite III subfamilies to the acrocentric chromosomes

The centromeres and the short arms of the five pairs of acrocentric chromosomes in humans are composed of tandemly ordered repetitive DNA. Previous studies have suggested that the exchanges between acrocentric chromosomes have resulted in concerted evolution of different DNA sequences in their short arms. The acrocentric chromosomes are clinically relevant since they are involved in Robertsonian translocation formation and non-disjunction resulting in aneuploidy. Here we have identified seven new satellite III repetitive DNA subfamilies, determined their nucleotide sequences and established their chromosomal distributions on the short arms of the acrocentric chromosomes. Knowledge of these related sequences may help to elucidate the molecular basis of Robertsonian translocation formation.

Near-haploidy and subsequent polyploidization characterize the progression of peripheral chondrosarcoma

Chondrosarcomas are malignant cartilaginous tumors arising centrally in bone (central chondrosarcoma), or secondarily within the cartilaginous cap of osteochondroma (peripheral chondrosarcoma). We previously used DNA flow cytometry to demonstrate that near-haploidy is relatively frequent in peripheral chondrosarcomas. We performed fluorescence in situ hybridization (FISH) to interphase nuclei using centromeric probes, a genome wide loss of heterozygosity (LOH) analysis, and comparative genomic hybridization on five peripheral chondrosarcomas. We demonstrated near-haploidy in two low-grade tumors with only one copy and LOH of most chromosomes. Few chromosomes are disomic, with retention of heterozygosity and overrepresentation at comparative genomic hybridization. One tumor contains both a near-haploid clone with chromosomes in monosomic and disomic state, and an exactly duplicated clone. Two high-grade tumors clearly demonstrate polyploidization because most chromosomes show LOH and two copies at FISH, whereas few chromosomes have four copies with retention of heterozygosity. Using DNA from a relative, we demonstrate that chromosome loss is random regardless of parental origin. Using FISH on paraffin slides, we exclude near-haploidy to result from meiosis-like division in binucleated cells, characteristic for chondrosarcoma. In conclusion, our results indicate that near-haploidy characterizes the progression from osteochondroma toward low-grade chondrosarcoma. Moreover, further progression toward high-grade chondrosarcoma is characterized by polyploidization.

Chromosomal abnormalities in Hodgkin's disease are not restricted to Hodgkin/Reed-Sternberg cells

Hodgkin and Reed-Sternberg cells are considered to represent the malignant fraction in Hodgkin's disease. Several studies have shown that the Hodgkin and Reed-Sternberg cells are chromosomally abnormal, but genetic data about the morphologically normal cell population in Hodgkin's disease are very limited. This latter cell population has therefore been examined for chromosomal aberrations, using the in situ hybridization (ISH) procedure, making use of DNA probes for chromosomes 1, 7, 8, 9, 11, 12, 15, 17, and 18. Nuclei were isolated from freshly frozen (10 cases) and paraffin-embedded (16 cases) biopsy samples and 1000 nuclei per case were evaluated. The cases of Hodgkin's disease were compared with reactive lymph nodes, which show aberrant chromosome copy numbers in less than 1 per cent of the cells. Using strict scoring criteria, nuclei in the tumour were found to show an abnormal genotype, in the range of 1-12 per cent, with trisomies occurring most frequently. No characteristic numerical chromosome abnormality was observed. ISH on 4 microns thick paraffin sections of six cases of Hodgkin's disease revealed numerical aberrations for chromosome 1 in cells which appeared to be morphologically normal. The genomically abnormal nuclei did not differ in morphology or size from the nuclei of morphologically normal cells, but differed considerably in size when compared with the nuclei of Hodgkin/Reed-Sternberg cells after the ISH procedure. Three of these six cases revealed a population of apparently normal cells with an aberrant copy number which differed notably from the fraction observed in reactive lymph nodes. It is concluded, therefore, that a subset of morphologically normal cells, next to the Hodgkin/Reed-Sternberg cells, are chromosomally aberrant and may participate in the malignant cell fraction of Hodgkin's disease.

Inherited interstitial duplications of proximal 15q: genotype-phenotype correlations

We present the cytogenetic, molecular cytogenetic, and molecular genetic results on 20 unrelated patients with an interstitial duplication of the proximal long arm of chromosome 15. Multiple probes showed that the Prader-Willi/Angelman critical region (PWACR) was included in the duplication in 4/20 patients, each ascertained with developmental delay. The duplication was also found in two affected but not in three unaffected sibs of one of these patients. All four probands had inherited their duplication from their mothers, three of whom were also affected. Two of the affected mothers also carried a maternally inherited duplication, whereas the duplication in the unaffected mother and in an unaffected grandmother was paternal in origin, raising the possibility of a parental-origin effect. The PWACR was not duplicated in the remaining 16 patients, of whom 4 were referred with developmental delay. In the 14 families for which parental samples were available, the duplication was inherited with equal frequency from a phenotypically normal parent, mother or father. Comparative genomic hybridization undertaken on two patients suggested that proximal 15q outside the PWACR was the origin of the duplicated material. The use of PWACR probes discriminates between a large group of duplications of no apparent clinical significance and a smaller group, in which a maternally derived PWACR duplication is consistently associated with developmental delay and speech difficulties but not with overt features of either Prader-Willi syndrome or Angelman syndrome.

Site-specific retrotransposition of L1 elements within human alphoid satellite sequences

In the course of a search for microsatellites as centromeric polymorphic markers at the 3' ends of Alu or L1 elements, we observed a much higher frequency of L1 than Alu elements embedded within alpha satellite DNA. By sequence analysis of the L1 elements at their alphoid locus of insertion, we found that the insertion site was specific, with the consensus being (Py)2-10/ (Pu)3-7. All potential sites within the consensus alphoid 171-bp repeat are occupied by such elements. This confirms the finding by Feng et al. (1996; Human retrotransposon encodes a conserved endonuclease required for retrotransposition, Cell 87:905-916) that the progenitor L1 elements encode a site-specific endonuclease and that they generate copies that are inserted at these specific sites. The analysis of retrotransposed L1 elements within the alphoid domains of the acrocentric chromosomes showed that a number of loci are shared among all five acrocentrics. This sheds light on the manner in which centromeric regions of these chromosomes are exchanging information during evolution.

SINE and LINE within human centromeres

A number of the Alu and L1 elements present within the centromeric regions of the human chromosomes have been analyzed by polymerase chain reaction amplification. The oligonucleotide primers were homologous to the 3' end consensus sequences of either Alu or L1 in conjunction with an oligonucleotide primer homologous to alphoid sequences specific to different chromosomes. This allowed one to detect an unusual number of Alu and L1 polymorphisms at different loci. It is proposed that this results from molecular rearrangements which occur within the alpha-satellite DNA in which they are embedded (Marçais et al. J. Mol. Evol. 33:42-48, 1991) and not because the centromeric regions are targets for new insertions of such elements. The same analyses were made on cosmids and YACs originating from the centromeric region of chromosome 21 as well as on a collection of somatic hybrids containing chromosome 21 centromere as unique common human genetic material. The results were consistent with the above hypothesis.

Human gamma X satellite DNA: an X chromosome specific centromeric DNA sequence

The cosmid clone, CX16-2D12, was previously localized to the centromeric region of the human X chromosome and shown to lack human X-specific alpha satellite DNA. A 1.2 kb EcoRI fragment was subcloned from the CX16-2D12 cosmid and was named 2D12/E2. DNA sequencing revealed that this 1,205 bp fragment consisted of approximately five tandemly repeated DNA monomers of 220 bp. DNA sequence homology between the monomers of 2D12/E2 ranged from 72.8% to 78.6%. Interestingly, DNA sequence analysis of the 2D12/E2 clone displayed a change in monomer unit orientation between nucleotide positions 585-586 from a "tail-to-head" arrangement to a "head-to-tail" configuration. This may reflect the existence of at least one inversion within this repetitive DNA array in the centromeric region of the human X chromosome. The DNA consensus sequence derived from a compilation of these 220 bp monomers had approximately 62% DNA sequence similarity to the previously determined gamma 8 satellite DNA consensus sequence. Comparison of the 2D12/E2 and gamma 8 consensus sequences revealed a 20 bp DNA sequence that was well conserved in both DNA consensus sequences. Slot-blot analysis revealed that this repetitive DNA sequence comprises approximately 0.015% of the human genome, similar to that found with gamma 8 satellite DNA. These observations suggest that this satellite DNA clone is derived from a subfamily of gamma satellite DNA and is thus designated gamma X satellite DNA. When genomic DNA from six unrelated males and two unrelated females was cut with SstI or HpaI and separated by pulsed-field gel electrophoresis, no restriction fragment length polymorphisms were observed for either gamma X (2D12/E2) or gamma 8 (50E4) probes. Fluorescence in situ hybridization localized the 2D12/E2 clone to the lateral sides of the primary constriction specifically on the human X chromosome.

Identification of amplified DNA sequences in breast cancer and their organization within homogeneously staining regions

A modified comparative genomic hybridization (mCGH) technique was used to identify and map amplified DNA sequences in six homogeneously staining regions (hsr) from three primary breast carcinomas. Five different chromosomal regions and bands were identified as sites of amplification: 8p1, 17q21.1, 17q23 (two cases), 19q13.3, and 20q13.3. The mCGH site located on 17q21.1 was demonstrated to correspond to a 50-100-fold amplification of ERBB2. Further in situ hybridization experiments were used to confirm the mCGH results and to characterize the organization of the amplified sequences within the hsr. In five of six instances, two or more chromosomal regions were found amplified in the same hsr. In the tumor with the less modified karyotype, the two hsr comprised DNA sequences from three different chromosomes and showed different patterns of amplification. In the tumor with the most rearranged karyotype, the hsr-carrying chromosomes were formed by the translocation and amplification of sequences from three or four different chromosomal sites. This illustrates the complexity of the amplification process in breast cancers.

Topographic changes in a heterochromatic chromosome block in humans (15P) during formation of the nucleolus

Fluorescence in situ hybridization and multispectral confocal laser scanning microscopy revealed a highly dynamic nucleolar-associated chromosome 15 satellite III heterochromatin cluster in humans. This nucleolar-associated DNA was highly decondensed at the metaphase plate compared with its topography at interphase and appeared to act as a centre for the post-mitotic reorganization of the nucleolus. Our data showed unexpected trans-mitotic changes in the topography of this nucleolar-associated satellite III DNA that suggest that this locus-specific heterochromatin superstructure may be involved in nucleolar organization.

Karyotypic heterogeneity and its relation to labeling index in interphase breast tumor cells

We have used fluorescence in situ hybridization (FISH) with chromosome-specific probes and immunofluorescent detection of in vivo bromodeoxyuridine (BrdUrd) incorporation to evaluate simultaneously numerical chromosome aberrations and proliferative activity of breast cancers. The number of distinct hybridization domains specific for repetitive pericentromeric sequences on chromosomes 1, 7, 11, 15, 17, and X was used as an indicator of copy number of these chromosomes in interphase tumor cells from 23 human breast cancers. Every tumor analyzed showed a heterogeneous distribution of copy number for at least one chromosome type. The copy number distribution for different chromosomes within a tumor frequently showed differing patterns. Major cell populations showing monosomy were relatively rare, occurring only in five cases for chromosome 17, once for chromosome 1, and once for chromosome 15. Flow cytometric analysis of DNA ploidy correlated well with FISH analysis, although flow cytometry failed to detect aneuploidy when only a few chromosomes were affected. To determine whether cell populations with different chromosomal copy numbers have identical proliferation characteristics in vivo, BrdUrd incorporation and centromeric copy number were detected simultaneously. Comparison of the chromosome copy number distribution in BrdUrd-positive cells vs. the distribution of the entire cell population showed different distributions in seven of the 20 cases analyzed. This study demonstrates the common occurrence of chromosome copy number heterogeneity and suggests that a cell phenotype (proliferation) may be associated with genotypic subpopulations.

Human ribosomal RNA gene cluster: identification of the proximal end containing a novel tandem repeat sequence

Human ribosomal RNA genes (rDNA) are arranged as tandem repeat clusters on the short arms of five pairs of acrocentric chromosomes. We have demonstrated that a majority of the rDNA clusters are detected as 3-Mb DNA fragments when released from human genomic DNA by EcoRV digestion. This indicated the absence of the EcoRV restriction site within the rDNA clusters. We then screened for rDNA-positive cosmid clones using a chromosome 22-specific cosmid library that was constructed from MboI partial digests of the flow-sorted chromosomes. Three hundred twenty rDNA-positive clones negative for the previously reported distal flanking sequence (pACR1) were chosen and subjected to EcoRV digestion. Seven clones susceptible to EcoRV were further characterized as candidate clones that might have been derived from the junctions of the 3-Mb rDNA cluster. We identified one clone containing part of the rDNA unit sequence and a novel flanking sequence. Detailed analysis of this unique clone revealed that the coding region of the last rRNA gene located at the proximal end of the cluster is interrupted with a novel sequence of approximately 147 bp that is tandemly repeated and is connected with an intervening 68-bp unique sequence. This junction sequence was readily amplified from chromosomes 21 and 15 as well as 22 using the polymerase chain reaction. Fluorescence in situ hybridization further indicated that the approximately 147-bp sequence repeat is commonly distributed among all the acrocentric short arms.

Analysis of antifading reagents for fluorescence microscopy

The utility of p-phenylenediamine, 1,4-di-azobicyclo-(2.2.2.)-octane, and the commercial products Citifluor, Slowfade, and Vectashield, antifading agents frequently used as mounting media for fluorescence in situ hybridization, was investigated. Fading curves for bound fluorochromes were recorded with digital microscopy, and relative fluorescence intensities of fluorochromes in solution were measured with an aperture defined measurement system. The three commonly used fluorochromes, fluorescein, tetramethyl rhodamine, and coumarin, were studied. Vectashield offered the best antifading properties for all three fluorochromes, although their relative fluorescence intensity was slightly less in Vectashield in comparison with other antifading agents. In Vectashield, fluorescein, tetramethyl rhodamine, and coumarin showed half-life times of 96, 330, and 106 s, respectively, whereas in 90% glycerol in PBS (pH 8.5), these half-life time values were 9, 7, and 25 s, respectively. Vectashield is particularly recommended as a mounting medium for quantitative digital imaging microscopy and for multicolor applications, where it is easy to have errors due to differences in fading rates of the fluorochromes.

Bladder irrigation specimens assayed by fluorescence in situ hybridization to interphase nuclei

Bladder irrigation specimens provide a sampling of the entire bladder urothelium and are the most practical sample for longitudinally monitoring patients. This study presents cross-sectional fluorescence in situ hybridization (FISH) analyses with correlated DNA cytometry data on 76 patients monitored for recurrent bladder tumors. FISH probes complementary to centromeric satellite sequences for chromosomes 1, 7, 9, 11, 15, and 17 were used. Aberrations in copy number were observed for chromosomes 1, 7, 11, and 17 principally in patients with aneuploid tumors. Monosomy of chromosome 9 was observed in 39% of the diploid and 31% of the specimens with high hyperdiploid fraction. Significantly, 24% of patients with a history of bladder cancer but with no clinical evidence of disease exhibited monosomy of chromosome 9. This suggests a persistent and significantly large population of abnormal cells in the absence of clinical evidence of disease. Loss of chromosome 9 relative to DNA ploidy was observed in 24% of patients with no evidence of disease, in 59% of patients with tumor, and in 79% of patients with histologically confirmed transitional cell carcinoma, grades 1-3. Loss of chromosome 15 was also observed in a large percentage of patients. Loss of chromosome 15 was observed in 41% of specimens from patients in whom no tumor was seen, in 38% of specimens from patients with tumor, and in 67% of specimens from patients with histologically confirmed transitional cell carcinoma. Results of this study document the use of bladder irrigation specimens as a specimen source for FISH analyses.(ABSTRACT TRUNCATED AT 250 WORDS)

Origin and biology of a testicular Wilms' tumor

A pure triphasic testicular Wilms' tumor, without teratomatous elements, was studied using multiple techniques. Carcinoma in situ (CIS), the characteristic precursor of testicular germ cell tumors of adults (TGCTs), was found in the adjacent parenchyma. Flow cytometric analysis showed a single hypotriploid tumor stem line. Karyotyping of the tumor revealed some numerical and structural abnormalities, including an i(12p), the chromosomal marker of TGCTs. In situ hybridization supported the karyotypic findings, and showed a similar numerical distribution in CIS and the tumor. Molecular analysis of the tumor illustrated that all short arms of chromosome 12, including i(12p), were of maternal origin. No 12q deletions were detected. In spite of complete loss of the paternal 11p13 band, the zinc finger regions and exons 2 and 6 of the WT1 gene contained no aberrations. Therefore, this tumor suppressor gene is not inactivated due to aberrations in the studied regions. In addition, all four WT1 alternative transcripts were expressed in the tumor. No aberrations were found in chromosomal bands 11p15.5, 16q22.1, and 16q24. Both parental alleles of the human imprinted genes H19 and IGF2 were expressed in the tumor. This is the first report on the chromosomal and molecular characterization of an extrarenal Wilms' tumor. Its germ cell origin was unequivocally demonstrated.

Rapid fluorescence in situ hybridization with repetitive DNA probes: quantification by digital image analysis

Fluorescence in situ hybridization (FISH) has become an important tool not only in cytogenetic research but also in routine clinical chromosome diagnostics. Here, results of a quantification of fluorescence signals after in situ hybridization with repetitive DNA probes are reported using a non-enzymatic hybridization technique working with a buffer system not containing any formamide or equivalent chemical denaturing agents. Following simultaneous denaturation of both cells and DNA probes, the renaturation time was reduced to less than 30 min. For one of the DNA probes reasonable FISH-signals were even achieved after about 30 s renaturation time. In addition, the number of washing steps was reduced drastically. As a model system, two repetitive DNA probes (pUC 1.77, D15Z1) were hybridized to human metaphase spreads and interphase nuclei obtained from peripheral blood lymphocytes. The probes were labelled with digoxigenin and detected by FITC-anti-digoxigenin. The hybridization time was reduced step by step and the resulting fluorescence signals were examined systematically. For comparison the pUC 1.77 probe was also hybridized according to a FISH protocol containing 50% formamide. By renaturation for 2 h and overnight two FISH signals per nucleus were obtained. Using shorter renaturation times, no detectable FISH signals were observed. Quantification of the FISH signals was performed using a fluorescence microscope equipped with a cooled colour charge coupled device (CCD) camera. Image analysis was made interactively using a commercially available software package running on a PC (80486). For the pUC 1.77 probe the major binding sites (presumptive chromosomes 1) were clearly distinguished from the minor binding sites by means of the integrated fluorescence intensity. For the two (pUC 1.77) or four (D15Z1) brightest spots on the metaphase spreads and in the interphase nuclei hybridized without formamide, integrated fluorescence intensity distributions were measured for different renaturation times (0.5, 15, 30 min). The intra-nuclear variation in the intensity of the two brightest in situ hybridization spots appeared to be slightly higher (CV between 16 and 32%) than the corresponding variation in the metaphase spreads (CV between 10 and 19%). For the D15Z1 probe FISH signals were detected after hybridization without formamide and 15 min and 30 min renaturation. Always four bright spots were visible and tentatively assigned on the metaphase spreads (presumptive chromosome 15 and 9). The intensity variation of each pair of homologues in a metaphase spread showed a CV of 14 or 15%, respectively, for the presumptive chromosome 15, and 8 or 9%, respectively, for the presumptive chromosome 9.

Do specific nucleotide bases constitute the centromere?

It is becoming increasingly clear that the underlying base composition of the DNA located in the centromere region is vastly different in different organisms. The chromosomes of related species or even the various chromosomes of the same species differ widely in their so-called centromeric DNA. Yet all centromeres appear physically alike and perform similar functions. The present communication proposes that the physical properties of the centromere are not due to its base composition but due to stereophysical make-up of the DNA segment constituting the centromere. This unique make up might reflect some physical parameter, like curvature, of the DNA present in the centromere constriction. It is further proposed that a proteinaceous factor, centromerase, is responsible for holding the centromeres as one unit until meta-anaphase.

Chromosomal localization of human satellites 2 and 3 by a FISH method using oligonucleotides as probes

Classical satellites I, II and III are composed of a mixture of repeated sequences. However, each of them contains a simple family of repeated sequences as a major component. Satellites 2 and 3 are simple families of repeated sequences that form the bulk of human classical satellites II and III, respectively, and are composed of closely related sequences based on tandem repeats of the pentamer ATTCC. For this reason, extensive cross-hybridizations are probably responsible for the similar in situ hybridization patterns obtained for satellites II and III. We have used a fluorescent in situ hybridization method with highly specific oligonucleotides for satellites 2 and 3, respectively, as probes. Our results show that satellite 2 is mainly located on chromosomes 1, 2, 10 and 16, whereas the major domain of satellite 3 is on chromosome 9. Furthermore, minor sites of satellites 2 and 3 are shown. Two-colour in situ hybridizations have enabled us to define the spatial relationships existing between the major domains of both satellites and centromeric alpha satellite sequences. These experiments indicate that the heterochromatin regions of chromosomes 1, 9 and 16 have different molecular organizations.

A rapid and simple method to isolate and characterize highly polymorphic markers from the centromeric regions of the human chromosomes

Using oligonucleotide primers complementary to the 3' ends of either the Alu or the L1Hs consensus sequences in conjunction with a primer complementary to alpha satellite subsets specific to different human chromosomes, it was possible to detect and characterize polymorphisms originating from the microsatellites which are often present downstream these repetitive elements. The methodology does not require cloning, sequencing or synthesis of specific primers. Centromeric location was confirmed by linkage analysis, in situ hybridization and sequencing. The method is proposed for the generation of polymorphic markers from all centromeric regions.

The organisation of repetitive sequences in the pericentromeric region of human chromosome 10

Three satellite DNA families are present in the pericentromeric region of chromosome 10; the alpha satellite and two 5 bp satellite families defined here as satellites 2 and 3. Pulsed field gel electrophoresis (PFGE) demonstrates that these sequences are organised into five discrete arrays which are linked within a region of approximately 5.3 Megabases (Mb) of DNA. The alpha satellite is largely confined to a 2.2 Mb array which is flanked on its p arm side by two 100-150 kb satellite 3 arrays and on its q arm side by a 900 kb satellite 2 array and a further 320 kb satellite 3 array. This linear order is corroborated by fluorescent in situ hybridisation analyses. In total, these arrays account for 3.6 Mb of DNA in the pericentromeric region of chromosome 10. These data provide both physical information on sequences which may be involved in centromere function and a map across the centromere which has the potential to link yeast artificial chromosome (YAC) contigs currently being developed on both arms of this chromosome.

Somatic pairing of centromeres and short arms of chromosome 15 in the hematopoietic and lymphoid system

Normal human bone marrow and peripheral blood leukocytes as well as malignant cells from a variety of leukemias and lymphomas, demonstrate somatic pairing of centromeres and p arms of chromosome 15 during interphase. This phenomenon, effected by sequences on the p arm and requiring the intranuclear transport of spatial domains for at least one of the homologs, was not seen in amniotic fluid cells, uterine cervical tissue or in tissue fibroblasts. These studies contribute to the recent evidence of somatic pairing of homologous chromosomes in man and provide support for mobile chromosomal domains in interphase. It appears that sequences on the p arm of chromosome 15, possibly the nucleolar organizing genes, are uniquely important in the maturation of benign and malignant cells of hemato-lymphopoietic origin.

Moving satellites and unstable chromosome translocations: clinical and cytogenetic implications

We describe 2 families in which acrocentric short arm material moved from one chromosome to another. In case 1, a meiotic event resulted in movement of an unusually large paternal 21p to chromosome 13 in the fetus. In case 2, a mitotic event resulted in fetal mosaicism. The short arm material from a paternal chromosome 15 moved to chromosome 14 in some of the fetal cells. Movement of acrocentric short arm material resulted from breakage and exchange in centromeric areas of repetitive DNA. We suggest the mechanism may be similar to that of previously reported "jumping" translocations. Failure to recognize movement of the short arms of acrocentric chromosomes can result in erroneous interpretation of prenatal cytogenetic results and of other cytogenetic assays dependent on acrocentric short arm polymorphisms.

Isolation and identification of a novel tandemly repeated DNA sequence in the centromeric region of human chromosome 8

EcoRI subclones, designated as 50E1 and 50E4, were independently obtained from a cosmid clone previously mapped to the centromeric region of human chromosome 8. Southern blot hybridization analyses suggested that both subclones contain repetitive DNA sequences different from the chromosome 8 specific alphoid DNA. DNA sequence analysis of the 704 bp insert of 50E1 and the 1,962 bp insert of 50E4 revealed that both inserts contained tandemly repeated units of approximately 220 bp. Fluorescence in situ hybridization studies confirmed these two subclones to be specifically located on the centromeric region of chromosome 8. A 220 bp consensus sequence, derived from nine monomeric repeats, showed no significant homology to alphoid consensus sequences or to other currently known human centromeric DNA sequence. Furthermore, no significant homology was found with any other DNA sequence deposited in the EMBL or GenBank databases, indicating that this chromosome 8 specific repetitive DNA sequence is novel. From slot blot experiments it was estimated that 0.013% of the human genome comprises 1,750 of these monomeric repeats, residing on the centromeric region of chromosome 8 in tandem array(s).

Molecular cytogenetic characterization of marker chromosomes found at prenatal diagnosis

The nature and origin of two de novo small marker chromosomes found at prenatal diagnosis were determined by fluorescence in situ hybridization using chromosome centromere-specific probes and chromosome-specific plasmid libraries. One marker was found in a mosaic state and was shown to be an i(18p). The second marker was characterized as an inv dup(22). We conclude that molecular cytogenetic analysis contributes to the identification of marker chromosomes and therefore facilitates genetic counselling and decision-making for the parents.

Efficient identification of marker chromosomes in 27 patients by stepwise hybridization with alpha-satellite DNA probes

Using a procedure involving stepwise hybridization of alpha-satellite DNA probes at various conditions of stringency, 33 marker chromosomes from 27 patients were identified. The markers were ascertained prenatally in fetal amniotic fluid and chorionic villi samples or postnatally in blood from liveborn children. The marker chromosomes first were characterized by cytogenetic techniques and later identified by fluorescence in situ hybridization. There were 14 bisatellited markers, 3 metacentric nonsatellited marker chromosomes, 2 nonsupernumerary sex-chromosomal rings, and 9 patients carrying markers that appeared to be small rings. Multiple stringency conditions were used for the identification of 14 supernumerary ringlike chromosomes detected in 8 patients. Ring-like markers were initially screened at low stringency and grouped into alpha-satellite families. Subsequent higher stringency hybridization led to marker identification. Ringlike chromosomes originated from chromosomes 1, 2, 8, 12, 13 or 21, 14 or 22, 15, 18, and X. Multiple ringlike markers ascertained in a single patient were determined to originate from different chromosomes.

Meiotic analysis by FISH of a human male 46,XY,t(15;20)(q11.2;q11.2) translocation heterozygote: quadrivalent configuration, orientation and first meiotic segregation

Understanding the segregational behaviour of reciprocal translocations in man is of both theoretical and clinical importance. Generally, information for genetic counselling is obtained from empirical data although knowledge of gametic output can now be obtained by karyotyping individual human spermatozoa. However, neither empirical studies nor sperm karyotyping data provide detailed information on how the combinations of normal, balanced and unbalanced gametes arise. For this knowledge of quadrivalent orientation and first meiotic segregation is required. We have used dual colour fluorescence in situ hybridisation (FISH) to identify normal and derived chromosomes during meiosis in testicular biopsy material from a 46,XY,t(15;20)(q11.2;q11.2) heterozygote. We were able to determine the frequencies of different quadrivalent structures at first metaphase (MI) and the proportion of first meiotic divisions subject to interstitial chiasmata. Having identified all 2:2, 3:1 and 4:0 segregation products at second metaphase, it was possible to correlate segregation categories with the various forms of MI quadrivalent possibly indicating their modes of orientation. Finally the ratios of normal:balanced:unbalanced gametes expected to be produced by this translocation heterozygote were calculated.

Complementarity of interphase and metaphase chromosome analysis in human renal tumors

Fluorescence in situ hybridization (FISH) was used as a complement to earlier cytogenetic studies of human renal tumors. Chromosome-specific para-centromeric probes were applied to cells disaggregated from tissue blocks of tumors, fresh samples from which had yielded cytogenetic results after short-term culture. Cells were dissociated from thick sections of paraffin-embedded, formalin-fixed tissues. Biotin-labeled probes specific for chromosomes 1, 3, 7, 11, 12, 15, 17, and the Y chromosome were applied in individual cases and were detected by fluorescence. Probes for chromosomes 1, 7, and 17 yielded clean signals with disomic control frequencies near 90%, and 97% of controls showed a single bright spot for the Y chromosome. The 9 cases selected all provided ample numbers of dissociated cells which were hybridized successfully, although some chromosomal signals were poor in individual cases. Abnormal copy numbers of chromosomes 1 and/or 17, not identified in culture, were observed in 7 cases. Trisomy 7 observed in culture was substantiated by FISH on the original tissues, as was loss of the Y, in each of 4 cases, respectively. Our results include limited validation of culture cytogenetics, evidence of selection in culture of tumor subpopulations, and demonstration that interphase cytogenetics by FISH is applicable to archival tissue blocks after prolonged periods of storage. Conditions of culture before harvest and inherent heterogeneity within tumors permit selection for nonrepresentative subgroups within tumors and emphasize the need for multiple approaches to evaluation.

Characterisation of a boundary between satellite III and alphoid sequences on human chromosome 10

Alphoid and satellite III sequences are arranged as large tandem arrays in the centromeric regions of human chromosomes. Several recent studies using in situ hybridisation to investigate the relative positions of these sequences have shown that they occupy adjacent but non-overlapping domains in metaphase chromosomes. We have analysed the DNA sequence at the junction between alphoid and satellite III sequences in a cosmid previously mapped to chromosome 10. The alphoid sequence consists of tandemly arranged dimers which are distinct from the known chromosome 10-specific alphoid family. Polymerase chain reaction experiments confirm the integrity of the sequence data. These results, together with pulsed field gel electrophoresis data place the boundary between alphoid and satellite III sequences in the mapping interval 10 centromere-10q11.2. The sequence data shows that these repetitive sequences are separated by a partial L1 interspersed repeat sequence less than 500bp in length. The arrangement of the junction suggests that a recombination event has brought these sequences into close proximity.

Detection of subtle reciprocal translocations by fluorescence in situ hybridization

Three different subtle reciprocal translocations were detected on long, well-banded chromosomes. The same translocations were examined using fluorescence in situ hybridization (FISH) with chromosome-specific libraries and unique DNA sequences. Our findings show that FISH allows rapid and unequivocal detection and characterization of this type of chromosome rearrangement. This approach is especially useful for prenatal diagnosis when one of the parents is a balanced carrier of such small fragment translocations.

Beta satellite DNA: characterization and localization of two subfamilies from the distal and proximal short arms of the human acrocentric chromosomes

beta satellite is a repetitive DNA family that consists of approximately 68-bp monomers tandemly repeated in arrays of at least several hundred kilobases. In this report we describe and characterize two subfamilies located exclusively on the human acrocentric chromosomes. The first subfamily is defined by a homogeneous approximately 2.0-kb higher-order repeat unit and is located primarily distal to the ribosomal RNA gene cluster, based both on fluorescence in situ hybridization to metaphase chromosomes and on filter hybridization analysis of translocation chromosomes isolated in somatic cell hybrids. In contrast, the second subfamily is located both distal and proximal to the ribosomal RNA gene cluster on the same acrocentric chromosomes. The DNA sequences of a number of monomers from these two subfamilies are compared to each other and to other beta satellite monomers to assess both inter- and intrasubfamily sequence relationships for these monomers.

Prenatal identification of small mosaic markers of different chromosomal origins

In situ hybridization using a series of alphoid DNA probes has demonstrated the origin of two small accessory mosaic marker chromosomes ascertained from 1079 amniocenteses. These markers appeared to be de novo, derived from acrocentric chromosomes, and identical by traditional cytogenetic staining (G, Q, C, AgNOR, Hoechst-distamycin). Molecular characterization showed that one marker had originated from chromosome 14, the other from chromosome 22. Clinical outcome in both cases was normal.