A repeating unit of the DYZ1 family on the human Y chromosome consists of segments with partial male-specificity

Use of fluorescent oligonucleotide probes for differentiation between Paracoccidioides brasiliensis and Paracoccidioides lutzii in yeast and mycelial phase

BACKGROUND

Fluorescence in situ hybridisation (FISH) associated with Tyramide Signal Amplification (TSA) using oligonucleotides labeled with non-radioactive fluorophores is a promising technique for detection and differentiation of fungal species in environmental or clinical samples, being suitable for microorganisms which are difficult or even impossible to culture.

OBJECTIVE

In this study, we aimed to standardise an in situ hybridisation technique for the differentiation between the pathogenic species Paracoccidioides brasiliensis and Paracoccidioides lutzii, by using species-specific DNA probes targeting the internal transcribed spacer-1 (ITS-1) of the rRNA gene.

METHODS

Yeast and mycelial phase of each Paracoccidioides species, were tested by two different detection/differentiation techniques: TSA-FISH for P. brasiliensis with HRP (Horseradish Peroxidase) linked to the probe 5' end; and FISH for P. lutzii with the fluorophore TEXAS RED-X® also linked to the probe 5' end. After testing different protocols, the optimised procedure for both techniques was accomplished without cross-positivity with other pathogenic fungi.

FINDINGS

The in silico and in vitro tests show no reaction with controls, like Candida and Cryptococcus (in silico) and Histoplasma capsulatum and Aspergillus spp. (in vitro). For both phases (mycelial and yeast) the in situ hybridisation showed dots of hybridisation, with no cross-reaction between them, with a lower signal for Texas Red probe than HRP-TSA probe. The dots of hybridisation was confirmed with genetic material marked with 4',6-diamidino-2-phenylindole (DAPI), visualised in a different filter (WU) on fluorescent microscopic.

MAIN CONCLUSION

Our results indicated that TSA-FISH and/or FISH are suitable for in situ detection and differentiation of Paracoccidioides species. This approach has the potential for future application in clinical samples for the improvement of paracoccidioidomycosis patients prognosis.

Analysis of the largest tandemly repeated DNA families in the human genome

Background

Tandemly Repeated DNA represents a large portion of the human genome, and accounts for a significant amount of copy number variation. Here we present a genome wide analysis of the largest tandem repeats found in the human genome sequence.

Results

Using Tandem Repeats Finder (TRF), tandem repeat arrays greater than 10 kb in total size were identified, and classified into simple sequence e.g. GAATG, classical satellites e.g. alpha satellite DNA, and locus specific VNTR arrays. Analysis of these large sequenced regions revealed that several "simple sequence" arrays actually showed complex domain and/or higher order repeat organization. Using additional methods, we further identified a total of 96 additional arrays with tandem repeat units greater than 2 kb (the detection limit of TRF), 53 of which contained genes or repeated exons. The overall size of an array of tandem 12 kb repeats which spanned a gap on chromosome 8 was found to be 600 kb to 1.7 Mbp in size, representing one of the largest non-centromeric arrays characterized. Several novel megasatellite tandem DNA families were observed that are characterized by repeating patterns of interspersed transposable elements that have expanded presumably by unequal crossing over. One of these families is found on 11 different chromosomes in >25 arrays, and represents one of the largest most widespread megasatellite DNA families.

Conclusion

This study represents the most comprehensive genome wide analysis of large tandem repeats in the human genome, and will serve as an important resource towards understanding the organization and copy number variation of these complex DNA families.

Male microchimerism in healthy women and women with scleroderma: cells or circulating DNA? A quantitative answer

Male DNA, of presumed fetal origin, can be detected in the maternal circulation decades after delivery and is referred to as fetal microchimerism (FM). We previously found quantitatively greater FM in the circulation of women with the autoimmune disease scleroderma (SSc) than of healthy women. However, it is unknown whether this difference is due to intact circulating cells or free DNA released from breakdown in disease-affected tissues. To distinguish the origin of FM, we developed a real-time quantitative polymerase chain reaction (PCR) assay for the Y-chromosome-specific sequence DYS14, and tested 114 women in peripheral blood mononuclear cells (PBMCs) and/or plasma. Fifty-seven controls and 57 SSc patients were studied, 48 and 43 of whom, respectively, had given birth to at least one son. Circulating FM was quantitatively greater in PBMCs from SSc patients (n = 39; range, 0.0-12.5 male genome-equivalent cells per million maternal cells), compared with healthy women (n = 39; range, 0.0-4.4; P =.03). In contrast, there was no difference between patients (n = 25) and controls (n = 22) in plasma, and no evidence of free DNA. FM was enriched among T lymphocytes compared with PBMCs (P =.01) in controls (n = 14), but not in SSc patients (n = 14); the latter finding was most likely due to immunosuppressive medications. In conclusion, this real-time quantitative assay showed that quantitative differences in the circulation of women with SSc are due to cells and not to free DNA. As FM was not uncommon in healthy women, including among T cells, and because graft-versus-host disease has similarities to SSc, these results also suggest that FM merits investigation in pheresis products used for stem cell transplantation.

From the simple detection of microchimerism in patients with autoimmune diseases to its implication in pathogenesis

Long-term persistence of fetal cells in parous women (fetal microchimerism, FM) as well as maternal cells in their offspring (maternal microchimerism, MM) have been reported. Systemic sclerosis (SSc), primary biliary cirrhosis (PBC), and Sjögren's syndrome (SS) share similar epidemiology with a predilection for females following childbearing years, with clinical similarities to chronic graft-versus-host disease, a known condition of chimerism. This led to the hypothesis that FM could be involved in the pathogenesis of autoimmune diseases. Initial investigations were conducted in SSc, where the hypothesis was supported by the more frequent occurrence and, quantitatively, a greater degree of FM in women with SSc compared to matched healthy women. Long-term persistence, however, of fetal cells in healthy women indicates that FM per se is not sufficient for causing SSc, but may be important in the context of other risk factors, such as genetic susceptibility and HLA relationship among host and nonhost cells. Contradictory results have recently been published for both PBC and SS and cause difficulty in drawing any conclusions about the role of FM in their pathogenesis. On the other hand, MM has been investigated as a risk factor in patients with systemic lupus (SLE) and juvenile dermatomyositis (JDM). A potential role of MM has been suggested in the pathogenesis of SLE. Recent publications also support the hypothesis that MM might lead to increased risks for JDM. In conclusion, contradictory results have been observed. This reflects a need for standardization of protocols and the selection of control populations. Detection of microchimerism has to be quantitatively studied in the context of genetic factors in order to study its relationship to the pathogenesis of autoimmune diseases.

Occurrence of gonadoblastoma in females with Turner syndrome and Y chromosome material: a population study

The presence of Y chromosome material in patients with Turner syndrome is a risk factor for the development of gonadoblastoma. However, no cases with gonadoblastoma or other ovarian malignancies have been found in epidemiological studies of cancer, morbidity, or mortality in Turner syndrome. We examined 114 females with Turner syndrome for the presence of Y chromosome material by PCR. Initially, five different primer sets were used. Y Chromosome-positive individuals were further examined with an additional four primer sets. We found 14 (12.2%; 95% confidence interval, 6.9-19.7%) patients who had Y chromosome material. The karyotype in 7 of these patients did not suggest the presence of Y chromosome material. Seven of the patients had been ovariectomized before entering the study due to verified Y chromosome material, whereas three patients were operated upon after the DNA analysis. The histopathological evaluations showed that 1 of the 10 ovariectomized patients actually had a gonadoblastoma. The rest of the patients did not have gonadoblastoma or carcinoma in situ on histopathological evaluation. Three patients (age, >50 yr) positive for Y chromosome material chose not to have ovariectomy performed, and detailed ultrasonographies did not suggest the presence of gonadoblastoma. The frequency of Y chromosome material is high in Turner syndrome (12.2%), but the occurrence of gonadoblastoma among Y-positive patients seems to be low (7-10%), and the risk may have been overestimated in previous studies, perhaps due to problems with selection bias. This study emphasizes the need for prospective unbiased studies.

Genomic distribution of 5' TTCCA 3' repeat motif and its diagnostic potential in human Y-chromosome-related anomalies

We have studied genomic distribution of a simple repeat motif 5' TTCCA 3' derived from the DYZ1 fraction of the human Y chromosome employing restriction fragment length polymorphism and in situ hybridization techniques. This has led us to develop a synthetic DNA based genetic marker specific to human genome. Randomly selected human genomic DNA from both sexes, digested with a total of 16 restriction enzymes, OAT20Y probe comprising four repeat units of 5'TTCCA 3' motif failed to reveal fragment length polymorphisms. In contrast, with most of the enzymes, several multilocus monomorphic bands and with a few enzymes, smeary signals were detected. In situ hybridization of the OAT20Y probe with human chromosomes revealed grains on the long arm of the Y chromosome, whereas the X-chromosome and autosomes showed random distribution of the grains without any preferential labeling in the centromeric or telomeric regions. The OAT20Y probe uncovers a 3.4 kb isomorphic band exclusively in the human male DNA digested with Hae III enzyme. Using the OAT20Y probe, we have detected the presence of Y chromosome in mosaic cell populations of Turner's patients with dysgenetic gonads and high levels of LS/FSH. The presence of Y chromosome in these patients has been associated with an increased risk of gonadoblastoma. The OAT20Y probe offers sensitivity and accuracy for the detection of Y-chromosome-bearing cells in a mosaic cell population and, consequently, help in better management of the patients.

Influence of mosaicism on sexing of human preembryos detected by the polymerase chain reaction

PURPOSE

Preimplantation sex determination using a single cell by the polymerase chain reaction (PCR) was investigated to elucidate the influence of mosaicism.

METHODS

The SRY and ZFX genes were coamplified as target sequences for the Y and X chromosomes, respectively. The sensitivity of the single and nested PCR method was examined initially followed by amplification of single amniocytes by the nested PCR. Then the sex of single blastomeres at the three- and nine-cell stages was determined by the nested PCR.

RESULTS

The nested PCR was 10(4)-fold more sensitive than the single PCR. Sex determination was possible in 97.5% (117/120) of the blastomeres tested. However, the correspondence rate for all blastomeres within a single embryo was only 60% (12/20 embryos). Among the remaining embryos for which sexing of all blastomeres was not consistent, only one blastomere showed findings indicating the presence of mosaicism (or pseudomosaicism).

CONCLUSIONS

At least two blastomeres need to be assessed when determining the sex of an embryo in order to avoid misdiagnosis due to mosaicism (or pseudomosaicism).

Parental origin of the X chromosome, X chromosome mosaicism and screening for "hidden" Y chromosome in 45,X Turner syndrome ascertained cytogenetically

Our study confirms the finding that about 85% of X chromosomes in Turner girls are maternally derived. A new observation is the detection of a high frequency of mosaicism (15%) in Turner girls who by cytogenetic analysis were thought to have a pure 45,X karyotype. DNA examination of the material was done by hybridization with digoxigenin labelled, non-radioactive probes, and PCR products for microsatellite analysis were run on polyacrylamide gels. We screened for the presence of "hidden" Y chromosome mosaicism, using the primers SRY, ZFY, DYZ3, DYZ1 and DYS132. Contrary to other reports using the PCR technique to unravel "hidden" Y chromosome mosaics, we did not find any positive cases. A precise technical protocol for these new techniques is given, and the advantages are discussed.

11q trisomy detected by fluorescence in situ hybridization

A patient with psychomotor developmental delay, multiple minor anomalies, congenital heart disease and left inguinal hernia is reported. His karyotype was 45,X/46,X,+mar (3:37 cells), and the marker chromosome was identified as t(Y;11)(q12;q14?) using fluorescence in situ hybridization and fluorescent chromosome painting. He was diagnosed as mosaic for de novo 11q trisomy.

Sexing of in vitro-fertilized preimplantation mouse embryos by the PCR method

The applicability of the dual PCR method to embryo sexing was examined with the aim of establishing a noninvasive method of preimplantation diagnosis for human genetic disorders. Mouse pre-embryos obtained by in vitro fertilization were studied. The Sry gene sequence and the myogenin sequence were amplified as the Y-specific and internal control sequences, respectively. Amplification of as little as 10 pg of mouse genomic DNA was possible with the dual PCR method, the sensitivity being 10-fold greater than that of the single PCR method. The sex was identified in 100% (24/24) and 96% (23/24) of the pre-embryos tested at the 16- and 4-cell stages, respectively. In addition, the sex of all four single blastomeres dissociated from 4-cell pre-embryos agreed in 76% (16/21) of the specimens tested and 94% (79/84) of dissociated blastomeres could be sexed. The sex of single blastomeres biopsied from pre-embryos at the 8-cell stage could be identified. After transfer of 13 male and 25 female sexed pre-embryos, six viable fetuses were obtained. Histological examination showed that all these fetuses were of the predicted sex. Sexing of biopsied single blastomeres by the dual PCR method was rapid and reliable, suggesting its feasibility for preimplantation diagnosis of in vitro fertilized human pre-embryos.

Sex-determining region Y (SRY) in a patient with 46,XX true hermaphroditism

Using a polymerase chain reaction method, a search for Y-specific DNA sequences was made in samples derived from tissues of a 46,XX true hermaphrodite. We found a sequence of SRY in the ovotestis, skin and leukocytes. Other DNA sequences, which covered the pseudoautosomal boundary region, amelogenin gene and DYZ1 locus of Y-chromosome were not detected. The SRY gene detected in the patient by the polymerase chain reaction was not detected by Southern blot analysis, using the SRY fragment as a probe. These findings suggest that in the patient there is a mosaicism of cells with and without part of the Y chromosome, including the SRY sequence. As the SRY sequence was responsible for the development of the gonadal primordium to the ovotestis, SRY seems essential for gonadal differentiation in testis development.

PCR detection of structurally abnormal Y chromosomes

Three probes each detecting a locus on the proximal long arm of the Y chromosome were partially sequenced. Thus, 3 sets of novel primers were developed which enable PCR detection of these 3 loci. Five previously reported primer sets, 3 on the short arm and each one on the centromere and the distal long arm, were mapped along with the novel three using a mapping panel consisted of 8 patients each with different structural abnormality of the Y chromosome. Now, PCR detection of these 8 loci covering an entire length of the Y chromosome has become possible enabling rapid screening of patients with Y chromosome aberrations.

Arrangement of DYZ1 and DYZ2 repeats on the human Y-chromosome: a case with presence of DYZ1 and absence of DYZ2

The composition of Yq-heterochromatin is dominated by the two repetitive sequences DYZ1 (4000 copies) and DYZ2 (2000 copies). Probes derived from these sequences can be used for sex determination and the structural analysis of aberrant Y-chromosomes. Using such probes Schmid et al., have recently proposed a regular interspersion of the two sequences in a ratio of 2:1 over the entire Yq12 chromosome region. By Southern analysis we investigated the DNA of a normal male, cytogenetically negative for Yq-heterochromatin. Applying the same probes as used by Schmid et al., only a small amount of DYZ1 material could be detected. The case presented indicates the presence of DYZ1 only in the Yq11-Yq12 junction region and excludes DYZ2 from any function relevant for normal male development.

Sex determination of forensic samples by dual PCR amplification of an X-Y homologous gene

Sex determination by polymerase chain reaction (PCR) analysis of the X-Y homologous amelogenin gene is highly reliable since the detection of an X-specific amplified fragment validates the procedure. Previously, we reported that 250 ng of template DNA are required for sex determination by this method. We report here a refinement of the technique to include dual PCR. Dual PCR using two sets of primers results in the detection of X- and Y-specific amplified fragments from as little as 0.005 ng of template DNA. This is a powerful technique for the analysis of trace forensic samples and its application is discussed.

Sex identification of forensic specimens by polymerase chain reaction (PCR): two alternative methods

Sex identification of forensic samples (bloodstains and decomposed tissue) by polymerase chain reaction (PCR) was investigated. Amplification of a segment of the amelogenin gene using a pair of primers revealed both Y- and X-specific bands at the same time. The gene has counterparts in both the X and Y chromosomes and a small deletion in the former made it possible to distinguish them. Analysis of the X-specific band is the most reliable method for sex identification. THe locus includes a single copy gene so a sample of 250 ng/tube of deoxyribonucleic acid (DNA) is required for identification. Amplification of part of the DYZ1 locus was attempted as an alternative method for analysis of infinitesimal amounts of sample. Even DNA from putrefied tissue could be analyzed by PCR because the locus consists of thousands of copies of repeating units pHY10.