Construction, analysis, and application to 46,XY gonadal dysgenesis of a recombinant phage DNA library from flow-sorted human Y chromosomes

A long-range restriction map of deletion interval 6 of the human Y chromosome: a region frequently deleted in azoospermic males

Deletion interval 6 (DI6) of the human Y chromosome, located at the distal end of the long arm euchromatic region, is required for normal spermatogenesis. About 10% of males with idiopathic azoospermia or oligospermia have microdeletions in this region. Six gene families, including RBMY (RNA binding motif, Y chromosome), DAZ (deleted in azoospermia), and four recently isolated genes, have been mapped to this interval. Genes from all of these families show testis-specific expression and are thus candidates for azoospermic factor (AZF). DI6 is also rich in Y-specific repetitive sequences, which may be responsible for its frequent deletion. To understand the sequence organization of this region, a 5-Mb restriction map was constructed based on YAC clones and was partially verified on genomic DNA. The locations of five gene family members, as well as numerous STSs, were determined. The map shows several inverted and direct repeats several hundred kilobases in size. The restriction map of DI6 will facilitate future mapping of deletion breakpoints in infertile males and elucidation of mechanisms behind frequent deletions.

A human moderately repeated Y-specific DNA sequence is evolutionarily conserved in the Y chromosome of the great apes

Evolutionary conservation of the human-derived moderately repeated Y-specific DNA sequence Y-190 (DYZ5) was investigated in the chimpanzee, orangutan, and gorilla. Southern blot analysis showed the presence of the sequence in the Y chromosome of all great apes. Pulsed-field gel electrophoresis and in situ hybridization revealed that the repeat is organized in one major block and confined to a small region of the Y chromosome of the three species. DYZ5 was assigned to the proximal short arm of the Y chromosome of the chimpanzee and orangutan and to the long arm of the Y chromosome of the gorilla. In light of its evolutionary conservation, DYZ5 may have an as yet undetermined structural function in the Y chromosome.

Deletion mapping of DNA segments from the Y chromosome long arm and their analysis in an XX male

Twelve DNA segments have been localized to the long arm of the Y chromosome and were assigned to three intervals by deletion mapping. Of these segments, six were from distal Yq11.23, which is supposed to contain a spermatogenesis locus. The physical mapping information was used to analyze an XX male who is positive for DNA sequences both from distal Yp and from Yq. Two of the twelve sequences from Yq (Y-198 and Y-253) were detected in this patient along with two of six short-arm segments tested. Long-range physical mapping placed Y-198 and Y-253 on a common 1100-kb BssHII fragment. In this patient, the long-arm sequences were assigned to distal Xp by in situ hybridization. The data suggest that this XX male derived from an unequal interchange between an X and an inverted Y chromosome presumed to have been present in the patient's father.

A physical map of the human Y-chromosome short arm

A physical map of the Y-chromosome short arm was constructed using DNA probes p19B, Y-286/la5, pZFY, Y-280, and Y-227. These probes hybridize with four NotI fragments of 400 kb (p19B and Y-286/la5), 350 kb, 1.9 Mb, and 3.0 Mb, respectively. The restriction fragments were shown to be adjacent to each other by analysis of NotI partial digests, overlapping restriction fragments, and/or the detection of rearranged restriction fragments in a 46,XX male. The present map covers approximately 5.6 Mb of contiguous DNA of Yp. Previously, the size of the pseudoautosomal region was estimated to be 2.3 Mb, and a 5.3-Mb NotI fragment containing Y-specific repeated DNA was assigned to proximal Yp. These and the present data account for approximately 13 Mb and thus for most of the DNA content of the Y short arm.

Breakage of the human Y-chromosome short arm between two blocks of tandemly repeated DNA sequences

Y-chromosomal rearrangements, a common cause of sex reversal in man, frequently occur between two blocks of repeated DNA. Both blocks are composed of 20-kb tandemly repeated Y-chromosome-specific DNA sequences. They are located in the proximal portion of the Y short arm on a NotI restriction fragment of approximately 5.3 Mb and on an MluI fragment of approximately 5.5 Mb. Chromosome breaks positioned between the two blocks were detected in two of three 46,XY females with deletions of Yp and in five of six 46,XX males positive for the repeat sequences. The rearranged NotI fragments in the 46,XX males were 4.4 Mb and the MluI fragments were 2.0 Mb in length. This indicates that breaks occur within a small region of Yp defined by the two blocks of specific repeated DNA sequences. The region between the two blocks thus appears to be a focus of structural lability in the human Y chromosome.

Structure of a hypervariable tandemly repeated DNA sequence on the short arm of the human Y chromosome

The structure of a repeated DNA sequence located on the short arm of the human Y chromosome is described. Genomic mapping and cloning in lambda or cosmid vectors show that the repeated sequence consists of units 20.3 x 10(3) base-pairs long that contain the three previously described DNA sequences: Y-156, Y-190 and Y-223a. Analysis of male genomic DNA by pulsed-field gel electrophoresis shows that the units are tandemly arranged and are organized into two blocks. The major block is hypervariable in size and alleles in the range approximately 540 x 10(3) to 800 x 10(3) base-pairs were detected. The minor block is not variable in size and is approximately 60 x 10(3) base-pairs long. Analysis of rearranged Y chromosomes shows that both blocks are located on the short arm of the chromosome. Most commonly, the major block is distal to the minor block, but the opposite arrangement is also found.

Characterization of Y chromosomal deoxyribonucleic acid fragments and translocations by Southern blot analysis

Hybridization of Y chromosome-specific probes to Southern blots of genomic deoxyribonucleic acid from patients with chromosomal variants permits direct and rapid characterization of the chromosomal content. We have used two single-copy Y chromosomal sequences specific for the short arm (47z and DP34) and one repeated sequence specific to the long arm (Y3.4) to study several patients with different types of sex chromosomal abnormalities, including three patients with gonadal dysgenesis and the karyotype 45,X/46,X + fragment, two females with Y autosomal translocations involving similar regions of the Y chromosome (46,XX,t(Y;14)(q11,p11) and 46,XY,t(Y;15)(q11,p11), two males with very small Y chromosomes (del(Y)(q12) and i(Yp], and a 45,X male with a small Y autosomal translocation. These techniques are more sensitive than chromosome banding and thus are an important adjunct to karyotyping for analysis of chromosomal content. For patients with gonadal dysgenesis and uncharacterized fragments, demonstration of Y chromosomal sequences identifies an important risk factor for the development of gonadoblastoma. For other patients, accurate identification of Y chromosomal content may facilitate prediction of the patient's phenotype.

Y-specific DNA sequences in male patients with 46,XX and 47,XXX karyotypes

Y chromosomal DNA sequences were detected in three of four 46,XX males and in one 47,XXX male. One reiterated Y chromosomal sequence, Y-190, was localized by in situ hybridization to the distal short arm of an X chromosome of the 47,XXX male. This result is compatible with the hypothesis that an aberrant X/Y interchange has occurred, most likely during paternal meiosis, and that this interchange accounts for Y chromosomal material and sex reversal in this 47,XXX individual.

Construction of a chromosome 16-enriched phage library and characterization of several DNA segments from 16p

A flow sorted chromosome 16-enriched recombinant library was produced to isolate DNA probes useful for constructing a linkage map of 16p, primarily for the study of adult polycystic kidney disease (APKD). The APKD locus has been mapped to chromosome 16 by linkage with the probe 3'HVR, which is located in the region 16p12----pter. Of the 48 single-copy fragments isolated from this new phage library, 39 (81%) were found to be chromosome 16 specific. Probes mapping to chromosome 16 were regionally localized by hybridizing to flow-sorted spot blots of translocation products from lymphoblastoid cell lines containing the rearrangements t(1;16) or t(11;16). Translocation breakpoints at 16p13.11 and 16p11.1 were utilized to subdivide chromosome 16 into three regions: Twenty-six probes were mapped to 16p11.1----16qter, two to 16p11.1----16p13.11, and eleven to 16p13.11----16pter. Probes from 16p were examined for their recognition of restriction fragment length polymorphisms (RFLPs). Seven polymorphic probes were found which recognized eleven RFLPs. Six of the seven probes have RFLPs which are reasonably informative (polymorphism information contents (PIC) of over 0.25). Two of these identify polymorphisms with three different alleles, one of which has a PIC value of over 0.4. These probes may aid in the diagnosis of APKD and contribute towards a linkage map of chromosome 16.

Direct hybridization to DNA from small numbers of flow-sorted nucleated newborn cells

A technique is described that allows direct hybridization to the DNA of cells flow sorted onto nitrocellulose filters, which obviates an intervening DNA isolation step. The feasibility of this technique for studying small numbers of cells is demonstrated with human cord blood, which has a high proportion of nucleated cells. The cells are stained with fluorescein-conjugated anti-HLe-l, a monoclonal antibody that recognizes mature leucocytes. Anti-HLe-l-positive cells are all nucleated, and a controlled, precise number of them may be sorted directly onto a nitrocellulose membrane. In cord blood, a small percentage of anti-HLe-l-negative cells are nucleated erythrocytes, which may also serve as a source of DNA. Studies were performed on male or female newborn cells flow sorted onto nitrocellulose membranes and hybridized with either a non-specific human repeat DNA probe or a Y chromosome-specific probe. Importantly, the sex of the newborn could be determined at the DNA level from as few as 50 sorted cord blood leucocytes or 5,000 HLe-l-negative cells. Since nucleated erythrocytes are common in fetal blood but rarely found in the peripheral circulation of adults, the method has potential application for the determination of fetal sex from analysis of flow-sorted nucleated erythrocytes present in the maternal circulation during pregnancy.

Y-190, a DNA probe for the sensitive detection of Y-derived marker chromosomes and mosaicism

A DNA probe (Y-190) is described that specifically hybridizes with repeated DNA sequences in the short arm of the human Y chromosome. The suitability of Y-190 to detect Y-derived DNA is shown in two patients with a 45,X/46,X+ marker karyotype and in a third patient previously described as having a 45,X karyotype.