Regional assignment of a 2.1-kb repetitive sequence to the distal part of the human Y heterochromatin

AT-rich repeats associated with chromosome 22q11.2 rearrangement disorders shape human genome architecture on Yq12

Low copy repeats (LCRs; segmental duplications) constitute approximately 5% of the sequenced human genome. Nonallelic homologous recombination events between LCRs during meiosis can lead to chromosomal rearrangements responsible for many genomic disorders. The 22q11.2 region is susceptible to recurrent and nonrecurrent deletions, duplications as well as translocations that are mediated by LCRs termed LCR22s. One particular DNA structural element, a palindromic AT-rich repeat (PATRR) present within LCR22-3a, is responsible for translocations. Similar AT-rich repeats are present within the two largest LCR22s, LCR22-2 and LCR22-4. We provide direct sequence evidence that the AT-rich repeats have altered LCR22 organization during primate evolution. The AT-rich repeats are surrounded by a subtype of human satellite I (HSAT I), and an AluSc element, forming a 2.4-kb tripartite structure. Besides 22q11.2, FISH and PCR mapping localized the tripartite repeat within heterochromatic, unsequenced regions of the genome, including the pericentromeric regions of the acrocentric chromosomes and the heterochromatic portion of Yq12 in humans. The repeat is also present on autosomes but not on chromosome Y in other hominoid species, suggesting that it has duplicated on Yq12 after speciation of humans from its common ancestor. This demonstrates that AT-rich repeats have shaped or altered the structure of the genome during evolution.

Characterization of a new aberration of the human Y chromosome by banding methods and DNA restriction endonuclease analysis

Comparative cytogenetic analyses were performed with ten different banding methods on a previously undescribed, inherited structural aberration of a Y chromosome, and the results compared with those of normal Y chromosomes occurring in the same family. The value of the individual staining techniques in investigations of Y chromosomal aberrations is emphasized. The aberrant Y chromosome analyzed can be formally derived from an isodicentric Y chromosome for the short arm with a very terminal long-arm breakpoint, in which the centromere, an entire short arm, and the proximal region on one long arm was lost. This interpretation was confirmed by determining the amount of the two Y-specific DNA sequences (2.1 and 3.4 kb in length) by means of Hae III restriction endonuclease analysis. The karyotype-phenotype correlations in the men with this aberrant Y chromosome, especially the fertility dysfunctions (oligoasthenoteratozoospermia, cryptozoospermia), are discussed. The possibility of the existence of fertility factors involved in the control of spermatogenesis within the quinacrine-bright heterochromatic region of the Y long arm is presented.

Distribution of DYZ2 repetitive sequences on the human Y chromosome

The distribution of the 2000 copies of the Y-specific repetitive family DYZ2 is controversial since previous reports have mapped these sequences to different sites of the Yqh region. In this work, we have performed non-radioactive in situ hybridization of a cloned DYZ2 fragment at higher stringency conditions on 5-aza-cytidine-enlarged Y chromosomes; the results suggest a non-uniform distribution of these sequences, which are preferentially located at the proximal and distal parts of Yqh, including the C+/Q- heterochromatin at the boundary with the euchromatic region.

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.

Ratio of fetal to maternal DNA is less than 1 in 5000 at different gestational ages in maternal blood

Using Southern hybridization with the DNA probe pY3.4, we were not able to detect fetal DNA in blood of 36 pregnant women carrying male fetuses. Gestational ages ranged from 8-40 weeks of pregnancy. Using the same DNA probe, we were able to detect the male-specific signal in experimental dilution series down to 1/5000 on autoradiograms. We conclude that the ratio of fetal DNA in maternal circulation, in contrast to previous estimations, must be lower than 1/5000.

Organization of DYZ2 repetitive DNA on the human Y chromosome

The location of the human Y-specific repetitive DNA sequence DYZ2 with HaeIII cleavage sites spaced at 2.1 kb was reexamined. Previous reports had mapped the 2000 DYZ2 copies to the very distal end of the heterochromatic Yq12 band. In the present study, a cloned DYZ2 fragment (pHY2.1) was used for Southern and slot blot analyses of male DNA as well as for nonradioactive in situ hybridization to chromosomes. DNA and metaphase preparations from 79 individuals with polymorphic or aberrant Y chromosomes were examined. DYZ2 repeats are not confined to the distal tip of Yq12, but extend through the entire heterochromatin of Yq12. In the naturally occurring length polymorphisms of Yq, the amount of DYZ2 sequence varies in proportion to the measured sizes of band Yq12. Explanations are presented for the fact that previous studies restricted the location of DYZ2 to the telomeric end of Yq12.

Sex determination of blood stains with a recombinant DNA probe: comparison with radioactive and non-radioactive labeling methods

A recombinant DNA probe hybridizing specifically to human repeat DNA sequence (pHY10) of which about 3000 copies are present on the Y chromosome was used for sex determination of degraded DNA samples of blood stains. Human blood stains of male and female origin were readily differentiated with the pHY10 DNA probe. This radioactive technique enabled reliable and sensitive sex determination from blood or dried blood stains greater than 20 years old. Less than 1 microliter of blood or 1 piece of 0.5 cm length thread of blood stain from cotton fabric was sufficient for the test using dot blot hybridization. Compared with the radioactive labeling method, the photobiotin labeling method showed one thirtieth to one fiftieth lower sensitivity and presented some problems which are expected to be resolvable.

Characterization of rearranged Y chromosomes in human testicular tumor cell lines

Cytogenetic analysis of four cell lines established from two different human testicular tumors revealed rearranged or missing Y chromosomes. Southern blot analysis and in situ hybridization with different Y-derived human DNA sequences revealed the existence of Y chromosomal material even in a line without a cytogenetically visible Y chromosome and clarified the composition of Y marker chromosomes.

Molecular characterization of a Y;15 translocation segregating in a family

We have used Y-specific and Y-derived DNA probes for in situ hybridization and Southern blotting analysis to characterize a Y;15 translocation showing normal Mendelian inheritance in a family. Cytogenetically there appeared to be an unbalanced translocation of Yqh to 15p; this translocation may be considered as a prototype of those translocations between Yq and the short arm of an acrocentric chromosome which have a population incidence of approximately 1 in 2,000. Our molecular studies showed that, in all probability, the breakpoints were near the border between Yq11.23 and Yq12, and in 15p11, respectively; the translocation is abbreviated t(Y;15)(q12;p11). Using the Y-specific probe pY431 in a quantitative Southern hybridization assay, normal females had no hybridization, female carriers and normal men had the same amount, and male carriers had twice that amount. Cytogenetic analysis and quantitative in situ hybridization using probes pY431 and pY3.4 were consistent with the hypothesis that the portion of Yq translocated to 15p comprised all of Yq12 and none of Yq11. The absence of Southern hybridization with probes specific for Yp and Yq11 confirmed this observation. Even though the family was ascertained through two brothers who both had schizophrenia and were carriers of the translocation, the clinical evaluation of a total of nine individuals with the translocation and five without it did not suggest its association with an abnormal phenotype.

Three cases of 45,X/46,XYnf mosaicism. Molecular analysis revealed heterogeneity of the nonfluorescent Y chromosome

Three patients with 45,X/46,XYnf mosaicism were investigated by Southern hybridization using both X- and Y-specific DNA probes. Our patients seem to be hemizygous for the X chromosomal loci tested. Single-copy and low-copy repeated Y chromosomal sequences assigned to the short arm, centromere, and euchromatin of the long arm have been detected in our patients, suggesting the Y chromosomal origin of the marker chromosome both in male and female cases studied. Densitometry of autoradiographs revealed a double dose of Yp-specific fragments of the DXYS1 locus. None of the patients tested showed either the 3.4- or the 2.1-kb Hae III male-specific repeated DNA sequences. It seems likely that the Ynf is a pseudodicentric chromosome with duplication of Yp and euchromatic Yq sequences, the Yq heterochromatin being lost. Our findings indicate structural heterogeneity of the marker chromosome and in addition provide further information on the relative position of DNA sequences detected by DNA probes 50f2, M1A, and pDP105.

Use of two different deoxyribonucleic acid probes to detect Y chromosome deoxyribonucleic acid in subjects with normal and altered Y chromosomes

Four experiments evaluated the sensitivity and specificity of molecular techniques to detect human Y chromosome deoxyribonucleic acid. In experiment I, electrophoretic separation of normal male deoxyribonucleic acid fragments after digestion with endonuclease Hae III revealed two male-specific bands of 3.4 and 2.1 kilobase (kb). These bands were not visible if the fraction of male deoxyribonucleic acid in mixed samples was less than 0.3. In experiment II, by means of a repetitive copy Y deoxyribonucleic acid probe (pS4) mapped to Yq12, a male-specific 2.3 kb band was detectable in mixtures of 2.5 ng of male deoxyribonucleic acid and 997.5 ng of 45,X female deoxyribonucleic acid. In experiment III, hybridization with the pS4 probe was performed on the deoxyribonucleic acid of 20 subjects with a normal or a variant Y chromosome. In experiment IV, deoxyribonucleic acid from the same subjects was hybridized to a single copy probe (4B-2) mapped to the Yq11 region. Deoxyribonucleic acid from category A subjects (n = 8) with cytologically normal Y chromosomes hybridized to both deoxyribonucleic acid probes. Deoxyribonucleic acid from category B subjects (n = 2), including a variant Y chromosome that was negative for Q-banding but positive for C-bands, hybridized with the distal pS4 and proximal 4B-2 probes. Deoxyribonucleic acid from category C subjects (n = 10) with variant Y chromosomes uniformly negative for Q- and C-bands, did not hybridize with the pS4 probe. Deoxyribonucleic acid from three of the 10 category C subjects did hybridize to the more proximal sequence-detecting 4B-2 probe. Deoxyribonucleic acid from the remaining seven subjects in category C did not hybridize with either of the deoxyribonucleic acid probes.

Pseudoisodicentric bisatellited extra marker chromosome (tetrasomy 22pter----q11, trisomy Yqh), derived from a maternal Y/22 translocation. Association between this tetrasomy and "cat eye" phenotypical features

A patient with multiple congenital anomalies suggestive of the "Cat eye" syndrome was found to have an extra marker bisatellited chromosome 22 derived from a maternal Y/22 translocation, identified by multiple banding patterns in cultures treated with DA. The proband's karyotype is 47,XX, + psu idic(22)(Yqter----Yq12::22p13----22q11::++ +22q11----22p13::Yq12----Yqter), t(22;Y)(p13;q12)mat., being tetrasomic for 22pter----q11, and trisomic for Yqh. Similarity between his clinical features and reported "Cat eye" cases, confirms that this region is responsible for the phenotypical expression of the syndrome.

Minute chromosomes replacing the Y chromosome carry Y-specific sequences by restriction fragment analysis and in situ hybridization

Two unrelated males, a 43-year-old man with azoospermia and a 4-year-old boy with stature at the 10th centile, had similar karyotypes: 46,X,min. The minutes, present in all cells analyzed, stained weakly with G-, C-, and Q-banding methods. To elucidate their origin we used molecular techniques: In HaeIII digests of total genomic DNA from both individuals, no Y-specific reiterated sequences were detected. However, restriction fragment analysis with probe pDP31 demonstrated that the patients' DNA contained the Y-specific fragment. In situ hybridization with the same probe showed that these sequences were present on the minute chromosomes and have not been translocated elsewhere.

A male with a monocentric Yq isochromosome and presence of a Yp-specific DNA sequence

We describe clinical features and laboratory findings in a physically and mentally retarded male with underdeveloped testes, a seemingly monocentric isochromosome of Yq but the presence of a Yp-specific DNA sequence at a single dose of unknown genomic localisation, and the presence of H-Y antigen at normal male titer. Our data contribute to the fine mapping of the human Y chromosome by correlating phenotypic features with results from karyotypic, immunologic, and molecular hybridisation analyses.

Deletion of the long arm of the Y chromosome and review of Y chromosome abnormalities

We report on a patient whose karyotype is 45,X/46,X,del(Y) (pter----q11.212). We also present a review of literature on the Y chromosome in which evidence is presented that there are genes on the Y chromosome that prevent Ullrich-Turner syndrome manifestations; aid in testes maturation and spermatogenesis; and affect height, tooth size, and bone maturation.

A re-examination of the case for homology between the X and Y chromosomes of mouse and man

Evidence is presented from the literature which suggests that in mouse and man, (1) synapsis between the X and Y is nonhomologous, (2) crossing over does not regularly occur between the X and Y, but is prevented by "precocious" desynapsis, and (3) normal disjunction of the X and Y is assured by an achiasmatic end association.

Hae III restriction of DNA from three cases with nonfluorescent Y chromosomes (45XO/46XYnf)

Hae III restriction patterns are reported in three cases with normal-sized but nonfluorescent Y chromosomes (XO/XYnf mosaics). The 3.4- and 2.1-kb fragment classes of reiterated Y chromosomal DNA were not present in the three cases. Mechanisms leading to these findings are discussed.

Prenatal identification of a deleted Y chromosome by cytogenetics and a Y-specific repetitive DNA probe

A very small sex chromosome was identified prenatally as a Y chromosome by using molecular hybridization in conjunction with conventional cytogenetics techniques. The combination of R-banding, Q-banding, distamycin-DAPI staining suggested that the chromosome might be a de novo deletion of the Y chromosome as the father's Y chromosome was normal. Restriction enzyme analysis of amniotic fluid cell DNA using a Y chromosome repetitive probe confirmed the origin of this chromosome.

Improved direct molecular diagnosis and rapid fetal sexing

Adaptations of the techniques of modern molecular biology to prenatal diagnosis has opened new avenues for the detection of genetic diseases. We have taken advantage of the rapid adhesion of colony forming cells in cultured amniotic fluid samples to develop an improved method for molecular diagnosis. By employing the cell adherence regime sickle cell diagnosis using Mst II can be undertaken directly. In addition, hybridization with a cloned repetitive sequence that is of Y origin and has limited autosomal homology permits rapid fetal sexing in 3 to 4 days without compromising conventional cytogenetic or biochemical analysis. This combination of techniques provides a useful adjunct to convential prenatal genetic diagnosis in the second trimester.

Genus specificity and extensive methylation of the W chromosome-specific repetitive DNA sequences from the domestic fowl, Gallus gallus domesticus

Two female-specific repeating DNA units of 0.6 kilobase pairs (kb) and 1.1 kb, produced by digesting the genomic DNA of the White Leghorn chicken with Xho I, were cloned by inserting them into the Xho I site of an Escherichia coli plasmid vector pACYC177. Two such recombinant plasmids, pAGD0601 and pAGD1101, containing a single 0.6-kb and 1.1-kb sequence, respectively, were used as molecular probes. In situ hybridization of the 3H-probes to the metaphase chromosomes from the female White Leghorn embryos revealed their localization in the W chromosome. Semiquantitative Southern blot hybridization with 32P-probes in excess indicated that the 0.6-kb unit and 1.1-kb unit were repeated approximately 14,000 and 6,000 times, respectively, in the W chromosome. The two units comprised about 46% of the W chromosomal DNA. These two repeating units were found in the female genomes of every line of Gallus g. domesticus tested and in the female genomes of three jungle fowl species (G. gallus, G. sonneratii, and G. varius) but not in three species belonging to other genera in the suborder Galli. Hha I sites in the 0.6-kb and 1.1-kb repeating units were shown to be extensively methylated and a significant fraction of the Hpa II sites in the 0.6-kb repeating units were also shown to be methylated in the female genome of the White Leghorn. Methylation patterns of Hpa II sites in or around the 0.6-kb repeating units examined by the Msp I digestion were similar in the various lines of domestic fowls and the two species of jungle fowls, but G varius (black or green jungle fowl) produced a different pattern of digestion with Msp I.

Characterization of a Y/15 translocation by banding methods, distamycin A treatment of lymphocytes and DNA restriction endonuclease analysis

A de novo 14/21 Robertsonian translocation and a familially inherited Y/15 translocation were observed in a male infant with anomalies of the external genitalia. The Y/15 translocation was confirmed by cultivating lymphocytes in a medium containing distamycin A and by determining the occurrence of the Y-specific DNA sequences by means of Hae III restriction endonuclease analysis. Any connection between the structural chromosomal abnormalities and the symptoms of the infant is highly improbable.

Clinical, cytological, and biochemical investigations in a case of an XX male

Lymphocytes and fibroblasts of an XX male were investigated to evaluate the etiology of this trait. DNA extracted from lymphocytes was digested with restriction endonucleases to probe for male specific DNA. There was no indication of such DNA fragments. The X-linked steroid sulfatase showed an activity of female controls while H-Y antigen was found in concentrations comparable to male controls. Cytological examinations excluded a mosaic between 46,XX and 46,XY cells. With the "high resolution banding" technique no evidence was found for a chromosomal aberration in our patient. It is therefore concluded that a "de novo" gene mutation leading to male development is the most suitable explanation for the present case of an XX male.

Structure and evolution of human Y chromosome DNA

Two repeated sequences account for 70% of the DNA of the human Y chromosome. They are located in the heterochromatin of the long arm. These sequences are related to others found on human chimpanzee and gorilla autosomes, and on the human X chromosome but have diverged in a characteristic way from the non Y copies. They have no detectable phenotypic effect when translocated to autosomes. We have cloned DNA from the human Y chromosome using fluorescence activated cell sorting. At least one single copy sequence is present on both the X and Y chromosomes.

Characterisation of a human Y chromosome repeated sequence and related sequences in higher primates

The human Y chromosome carries 2000 copies of a tandemly repeated sequence, 2.47 kb long, which constitutes about 20% of the DNA of this chromosome. These sequences are localised on the tip of the long arm of the Y chromosome. Related sequences are present in DNA of females with a related but distinguishable restriction pattern. These autosomal sequences are distributed in tandem arrays on a number of autosomes. Related sequences are also present in gorilla and chimpanzee. In gorilla they resemble the human sequences in their restriction map but are not found on the Y chromosome whereas in chimpanzee the related sequences behave as a 'dispersed' repeat. Changes in the level of methylation of this sequence in different tissues of human males can be detected with the lowest levels found in sperm and placental DNA.

BrdU-Hoechst-Giemsa analysis of DNA replication in synchronized lymphocyte cultures. Study of human X and Y chromosomes

The combination of a technique of reversible methotrexate (MTX) imposed G1/S block in cultures of human lymphocytes with the BrdU-Hoechst-Giemsa technique permitted the study of DNA replication patterns in individual chromosomes at different intervals of the S phase in a cell cohort with uniform S + G2 duration. The procedure did not increase either the frequency of chromosomal breakage or SCE frequency. The technique applied permitted visualization of the banding pattern in over 90% of mitoses. Examination of mitosis following different times of exposure to BrdU revealed a high degree of synchrony in the progression of the cell cohort examined through the S phase. The presence of two distinct late replication patterns of the allocyclic X chromosome was confirmed in studies on lymphocytes from normal human females by this technique. Interindividual and intercellular differences of the replication pattern have been demonstrated. The replicating patterns from one individual were relatively constant. The analysis of the Y chromosome has revealed marked differences of the termination of replication in individual cells. Euchromatic regions have been shown to complete DNA synthesis first, followed by the distal part of the long arm and, finally, by the region of Yq11/Yq12 junction. Lateral asymmetry was localised at this region.

Patterns of exchange induced by mitomycin C in C-bands of human chromosomes. II. High frequency of Y-Y exchange in XYY cells

In XY cells, exchanges in the Y C-band were rare (less than 0.8%). However, in XYY cells we observed 58 Y chromosomes involved in exchange out of 208 (28%). Most were Y-Y interchanges. Therefore mitomycin C does affect Y C-bands, but subsequent interchange requires the presence of a homologue. This may be the consequence of interphase association of the homologues, or by homologous interaction of an affected DNA sequence in the two Ys. If the latter, the proposed sequence cannot be localized to proximal or distal parts of the Y C-band, as exchange points were observed in both. Also, it may be oriented in one direction in the Y, as the Y-Y exchanges which could be unambiguously classified were X-type events.