Short stature and azoospermia in a patient with Y chromosome long arm deletion

We report on a 42-year old male with short stature, azoospermia and a wide deletion of long arm of Y chromosome. On physical examination, the patient showed height of 149 cm (< 1 degree centile) and reduced volume (3 ml) and consistency of the testes. On hormonal evaluation, he showed increased serum gonadotropins and normal serum testosterone levels though its HCG stimulated levels were limited. Serum thyroid hormones were normal. Serum GH levels in baseline evaluation as well as after GHRH and GHRH + pyridostigmine administration were normal. Serum IGF I levels were lower than normal in baseline evaluation whereas its response to the GH administration was in the normal range. The bilateral testicular biopsy showed tubular atrophy, hyalinosis, interstitial sclerosis and a histological picture of a Sertoli cell only syndrome. Moreover the patient showed arthropathy, otopathy, small chin, small mouth and truncal obesity. On genetic evaluation, the patient showed a 46,X,delY (pter--q11.1:) karyotype and loss of several DNA loci on Yq. In fact he preserved short arm SRY, centromeric DYZ3 and more proximal euchromatic region Yq loci, including DYS270, DYS271, DYS272, DYS11, DYS273, DYS274, DYS148, DYS275, and missed more distal DNA loci from DYS246 to DYZ2. These results disclosed a wide Y long arm deletion, including all hypothized Yq azoospermia loci (except for AZFa and probably for one of the RBM genes, which lie proximally to the deletion) and possibly the Y-specific growth control region (GCY), mapped between DYS11 and DYS246 loci. This deletion is responsible for the complete azoospermia of the patient and probably also for his short stature, even if other factors could be implicated in the statural impairment. It further possibly allowed to relate the GCY gene(s) to the control of GH or IGF-I receptor or post-receptor pathway, being the alteration of this gene(s) consistent with the hormonal pattern of the patient.     

Deletion of HMG17 in uterine leiomyomas with ring chromosome 1

Uterine leiomyomas are characterized by several subgroups with characteristic chromosomal aberrations, mainly 12q14-15, 6p21, or interstitial deletions of chromosomes 3 and 7. For the first two subgroups, aberrations of the HMGIC and HMGIY genes have been described and are held responsible for tumor initiation. For other subgroups no molecular findings have been described as of yet. We focus here on a smaller subgroup of uterine leiomyomas with a ring chromosome 1 either as the only karyotypic deviation or occurring along with other abnormalities. In the p-arm of chromosome 1 HMG17, another member of the high-mobility group of proteins has been localized to the short arm of chromosome 1 (1p35) with two PAC clones on metaphase spreads of a uterine leiomyoma ring(1). Hybridization signals for these probes were not detected within the ring chromosome consistent with loss or deletion of HMG17. These findings suggest that HMG17 does not play a mechanistic role in leiomyoma similar to that observed with other high-mobility proteins.     

A sex reversal infant with XX karyotype and complete male external genitalia

The unusual case of a Japanese newborn XX male is presented. Examination of chromosomes in amniotic fluid cells had shown a normal female karyotype (46,XX), but ultrasonography revealed a penis and a scrotum. The neonate had normal male external genitalia, and serum levels of luteinizing hormone, follicle stimulating hormone, and testosterone were all within the normal range. High resonance chromosome analysis revealed an excess portion on the short arm of one of the X chromosomes. We examined his genomic DNA by polymerase chain reaction (PCR) and detected two Y specific regions in his genomic DNA, the sex-determining region Y (SRY) and pseudoautosomal boundary Y. Nucleotide sequencing of the PCR products of SRY indicated no mutation. These findings suggested that the translocation or insertion of an SRY region on the X chromosome led to the development of testicles and a male phenotype.     

Chromosomal polymorphism of the yeast Yarrowia lipolytica and related species: electrophoretic karyotyping and hybridization with cloned genes

Significant differences in electrophoretic karyotyping patterns were found among 27 strains of Y. lipolytica. Twenty-one of these strains were classified into four groups of similar karyotypes while six strains showed unique karyotypes. Chromosomal DNAs of different strains were hybridized with cloned genes of Y. lipolytica (URA3, LEU2, ARS18 and ARS68), which revealed four different bands in most strains. We conclude that the haploid chromosome number of Y. lipolytica is at least four, and possibly five or six. Electrophoretic karyotyping and hybridization with cloned genes of Y. lipolytica provided evidence of a large divergence between Y. lipolytica and related species of Saccharomycopsis, Endomycopsella and Endomyces.     

Human histone gene organization: nonregular arrangement within a large cluster

We have previously located the genes of the five human main type H1 genes and the gene encoding the testicular subtype H1t to the region 21.1 to 22.2 on the short arm of chromosome 6. To investigate the organization of the histone genes in this region, we isolated two YACs from a human YAC library by PCR screening with primers specific for histone H1.1. This screen revealed two YAC clones, YAC Y23 (corresponding to ICRFy901D1223) contains an insert of about 480 kb, whereas the smaller YAC 4A (corresponding to ICRFy900C104) spans about 340 kb and is completely covered by YAC Y23. We have subcloned the YAC inserts in cosmids, determined the linear orientation of the cosmids by cosmid walking, and constructed a restriction map of the entire region by mapping the individual cosmids using partial digests and hybridization with labeled oligonucleotides complementary to the cos site of the vector. Hybridization analysis, subcloning, restriction mapping, and sequencing revealed that most of the previously isolated phage and cosmid clones containing histone genes are part of this YAC including the clones containing the four human main type H1 histone genes H1.1 to H1.4, the H1t gene, and core histone genes. Thirty-five histone genes map within 260 kb of the YAC Y23 insert. All newly identified histone genes were sequenced, and the sequences were deposited with the EMBL nucleotide sequence database. The histone H1.5 gene is not part of this region, and we therefore conclude that the H1.5 gene and the associated core histone genes form a separate subcluster within this chromosomal region.     

The azoospermic factor on the Y chromosome

Azoospermia is the most frequent cause of male infertility. After excluding the obvious urological reasons and the effect of Klinefelter's syndrome, azoospermia may be caused by an abnormality in the crucial gene(s) expressed during male germ cell differentiation. Recently, two candidate genes for azoospermia have been cloned from the azoospermic factor (AZF) locus on the Y chromosome long arm (Yq). One is YRRM (Y chromosome RNA recognition motif) gene, and the other is DAZ (deletion in azoospermia) gene. Both genes encode RNA binding protein and their expression is restricted to the testis. Therefore they are good candidates for AZF, although their function remains unclear. Here, the genes on the Y chromosome possibly involved in spermatogenesis and the role of the Y chromosome in evolution are discussed.     

Part of the RBM gene cluster is located distally to the DAZ gene cluster in human Yq11.23

Normal human Y and inverted Y chromosomes were chosen for physical fluorescence in situ hybridization (FISH) mapping of RBM and DAZ probes for the relative positioning of the RBM and DAZ gene clusters in interval 6 of the human Y chromosome. The inversion breakpoint in Yq11.23 turned out to be distal to the DAZ gene cluster, as the entire DAZ signal appears in the short arm of the inv(Y) chromosome. On the contrary, this inversion breakpoint in Yq11.23 divides the RBM signal cluster, leaving a weaker signal on the long arm while bringing the main RBM signal to the short arm of the inv(Y) chromosome. Thus, it can be concluded that, in contrast to previous claims, part of the RBM gene cluster is located distally to the DAZ gene cluster in deletion interval 6 of the human Y chromosome.     

Fertility in mice requires X-Y pairing and a Y-chromosomal "spermiogenesis" gene mapping to the long arm

There is accumulating evidence that the mammalian Y chromosome, in addition to its testis-determining function, may have other male limited functions, particularly in spermatogenesis. We have previously shown that the short arm of the mouse Y carries information needed for spermatogonial proliferation. This information, together with the testis-determining gene Sry, is contained within the Y-derived sex reversal factor Sxra. XO males carrying a copy of Sxra attached to the X chromosome are nevertheless sterile owing to an almost complete arrest during the meiotic metaphase stages. Here we show that this meiotic block can be overcome by providing a meiotic pairing partner (with no Y-specific DNA) for the XSxra chromosome. However, this does not restore fertility because the sperm produced all have abnormal heads. It is concluded that the Y-specific region of the mouse Y chromosome long arm includes information essential for the normal development of the sperm head.     

Nonfluorescent Y chromosomes. Cytologic evidence of origin

Twelve presumptive structurally altered Y chromosomes were studied with Q-, G-, G-11, C-, Cd, and lateral asymmetric banding techniques and were compared with normal X and Y chromosomes and with an abnormal [i(Yq)] Y chromosome that exhibited intact fluorescence. Significant to this work is the fact that the Y chromosome has a small block of Giemsa-11 heterochromatin adjacent to the centromere on the long arm, while the X chromosome does not, which allows a distinction between the X- and Y-derived chromosomes. Two of the twelve altered chromosomes of either X or Y origin are small nonfluorescent rings. Each ring has a G-11-positive band of heterochromatin at the centromere, confirming Y origin. Each of the normal-length nonfluorescent presumed Ys and a Y with a fluorescent band in the center have one G-11 band at the centromere and another at an equal distance from the end of the long arm, the bands also being Cd positive, indicating that these chromosomes are pseudodicentric. The likely mechanism of origin is a break at the distal bright heterochromatin/euchromatin junction (or within the bright segment in the chromosome with the bright center band), fusion of the sister chromatids at the breakpoints, and loss of the distal segment.     

Genetic alteration mapping on chromosome 7 in primary breast cancer

Alterations of chromosome 7 are among the most frequent cytogenetic abnormalities found in human breast carcinoma. We examined genetic changes on chromosome 7 in 113 primary human breast tumors, using both microsatellite and restriction fragment length polymorphism/variable number of tandem repeats polymorphism markers mapping to the long arm (15 markers) and the short arm (8 markers). Allelic imbalance at 1 or more loci was observed in 50 (44%) of 113 tumors on the long arm of chromosome 7 and in 41 (36%) tumors on the short arm. Genetic changes of one arm were significantly associated with alterations of the other arm. The 50 7q-altered tumor DNAs exclusively showed a loss of heterozygosity (LOH), 23 (46%) at all informative loci tested on 7q and 27 (54%) at some loci (interstitial and/or telomeric deletions on 7q). The pattern of LOH of these 27 tumors enabled us to identify 3 distinct consensus regions of deletions on 7q, only 1 of which (7q31 region) has already been described in breast cancer. Among the 41 7p-altered tumor DNAs, 32 had a gain and/or loss of the entire short arm of chromosome 7. Fourteen tumor DNAs showed an allelic gain, and 18 tumor DNAs showed a LOH at each locus on the short arm. The other 9 7p-altered tumors showing partial random alterations of chromosome 7p revealed no common altered regions. This is the first report of an association between alterations of DNA sequences on chromosome 7p and breast cancer. The results suggest that tumor suppressor genes are present on the long arm of chromosome 7 and are associated with breast tumorigenesis. Moreover, the frequent loss or gain of a whole copy of chromosome 7p suggests the involvement of a gene dosage effect of this chromosomal arm in the pathogenesis of breast cancer.     

Glycosyltransferases in SWISS-PROT

We analyzed DNA from a patient with azoospermia whose Y chromosome was cytogenetically normal. A total of 16 loci on the Y chromosome long arm were examined: 15 loci between DYS7E and DYZ1, and the Y chromosome RNA recognition motif (YRRM1) locus, a candidate gene for the azoospermic factor AZF. We did not detect the YRRM1 gene in this patient. This finding supports the theory that YRRM1 is an essential gene for spermatogenesis.     

A de novo satellited short arm of the Y chromosome possibly resulting from an unstable translocation

A satellited long arm of the Y chromosome (Yqs) is considered a normal variation, whereas the presence of a satellite on the short arm of the Y (Yps) has never been described in the literature. A Yps chromosome could be clinically significant if the translocation resulting in Yps has relocated the testis-determining gene, SRY, to another chromosome. A carrier of such a translocation would therefore be at increased risk for having XX male and XY female offspring. Here we describe the first reported case of de novo Yps present in a phenotypically normal male. This Yps chromosome was positive for C-banding and nucleolus organizer region (NOR) staining and showed a hybridization signal for the beta-satellite sequence. Fluorescence in situ hybridization (FISH) analysis indicated that SRY was retained on the Yps and the translocation breakpoint on Yps was distal to the pseudoautosomal region. At prenatal diagnosis, a normal appearing Y chromosome was found in his son, and thus the satellite on Yps was lost during meiotic Xp-Yp pairing. This Yps chromosome was likely the product of an "unstable" translocation.     

Seven genes from human chromosome 18 map to chromosome 24 in the bovine

Bovine sequence tagged sites (STSs) were developed for seven genes and used for synteny mapping with a hybrid bovine x rodent cell line panel. The genes were thymidylate synthase (TYMS), pituitary adenylate cyclase activating peptide (ADCYAP1), and melanocortin-2 receptor (MC2R) from the short arm of human chromosome (HSA) 18 and N-cadherin (CDH2), transthyretin (TTR), gastrin-releasing peptide (GRP), and plasminogen activator inhibitor 2 (PAI2) from the long arm of HSA 18. Primers for these genes were designed with human, ovine, or bovine sequences aligned with a sequence from a second species. The bovine PCR product was cloned, and the fragment was sequenced to verify that the homologous gene was indeed amplified. A second set of bovine-specific PCR primers were developed for each gene from these sequences. These STSs were used for synteny mapping, and all seven genes were syntenic with markers of bovine chromosome (BTA) 24. The concordance with BTA 24 was at least 96.5% for all genes.     

Prenatal identification of mos 45,X/46,X,+mar in a normal male baby by cytogenetic and molecular analysis

We report a case of mos 45,X/46,X,+mar, diagnosed prenatally by amniocentesis, whose physical examination, including external and internal organs, along with serum testosterone values were normal five years after delivery. The mosaic karyotype was seen in 146 of 240 cells examined (amniotic fluid cells, 110/65; placental chorionic villi: 5/4; cord blood, 21/81; cultured skin fibroblasts, 10/90) from 386 metaphases, and the marker chromosome appeared as a small non-fluorescent acrocentric chromosome. All autosomes appeared normal, and no normal Y chromosome could be demonstrated. Analysis of 26 Y-chromosome loci by molecular techniques such as PCR, Southern analysis using multiple Y-specific DNA probes, and Hae III restriction endonuclease assessment of male-specific repeated DNA in the heterochromatic region of the Y chromosome, and fluorescence in situ hybridization (FISH), revealed the marker was derived from a Y chromosome including p terminal to q11.23, and paracentric inversion in the remaining Y long arm. The formation of testes can be considered as existence of SRY (sex-determining region of Y) as a testis-determining factor. The present report illustrates the importance of FISH and molecular techniques as a complement to cytogenetic methods for accurate identification and characterization of chromosome rearrangements in prenatal diagnosis.     

Mapping the locus of the H-Y gene on the human Y chromosome

The H-Y locus is on the short arm of the human Y chromosome in most individuals but on the long arm in at least one of 17 individuals with structural abnormalities of the Y.     

Different patterns of variation at the X- and Y-chromosome-linked microsatellite loci DXYS156X and DXYS156Y in human populations

We compared the global pattern of variation at two homologous microsatellites mapping to the long arm of the X chromosome (DXYS156X) and to the short arm of the Y chromosome (DXYS156Y) in humans. A single pair of oligonucleotide primers amplifies these two nonallelic loci, each of which contains polymorphism in the number of pentanucleotide units. We observed 11 alleles in a sample of 2290 X chromosomes and 2006 Y chromosomes from 50 populations representing 6 major geographic regions. The overlapping size range of the X- and Y-chromosome alleles indicated a more complex distribution of alleles at these two loci than previously reported. Contrasting patterns of X-chromosome-linked and Y-chromosome-linked variation were reflected in statistically significant differences in genetic diversity values among geographic regions and between X and Y chromosomes. Higher levels of diversity characterized the DXYS156X locus in Africa (0.799 +/- 0.004) and the DXYS156Y locus in East Asia (0.700 +/- 0.006) compared with populations from other regions. These different patterns of variation can be explained by a combination of processes at both the molecular and population levels, including variable mutation rates, different effective population sizes, and genetic drift.     

Giemsa-banding and the identification of the Y/autosome translocation in the african marsh mongoose, Atilax paludinosus (Carnivora, Viverridae)

The diploid chromosome number of 35 in the male and 36 in the female African marsh mongoose, Atilax paludinosus, has been confirmed. C- and G-banding analyses have shown that the Y chromosome is probably translocated onto the proximal end of the acrocentric partner of a heteromorphic autosomal pair (C3). The other partner is a subtelocentric with a heterochromatic short arm. During the translocation process, this short arm was removed and presumably lost. The sex determining mechanism in Atilax could be written as XX in the female and XYA-A in the male.     

The proopiocortin (adrenocorticotropin/beta-lipoprotein) gene is located on chromosome 2 in humans

The proopiocortin gene is located on chromosome 2 in humans. A 13-kb DNA fragment containing proopiocortin gene sequences was identified in human cells while proopiocortin-related genes sequences of 9.8 and 6.2 kb were present in mouse cells. In human-mouse cell hybrids which contained reduced numbers of human chromosomes and a complete set of mouse chromosomes, the 9.8- and 6.2-kb fragments were always present while the 13-kb fragment segregated with human chromosome 2 and the chromosome 2 enzyme markers acid phosphatase-1 (ACP1), malate dehydrogenase-1 (MDHI), and isocitrate dehydrogenase-1 (IDH1). Analysis of a single cell hybrid with a broken chromosome 2 indicates that the proopiocortin and ACP1 genes are closely linked and in the distal region of the short arm of chromosome 2.     

Quantitative FISH by image cytometry for the detection of chromosome 1 imbalances in breast cancer: a novel approach analyzing chromosome rearrangements within interphase nuclei

Interphase cytogenetics have become a widespread tool for investigation of chromosome rearrangements in solid tumors. The most recurrent chromosome alteration within breast cancer affects chromosome 1, leading principally to gain of the long arm and/or loss of the short arm. We have developed a new method for detection of chromosome 1 arm imbalances in interphase nuclei. The method is based on quantitation of the fluorescence signals emitted by the hybridized two-color paintings of the short and long arms using image cytometry. The chromosome arm imbalance was determined by calculating the ratio of both fluorescence emissions of each arm. The ratio of the paintings of normal lymphocytes was used as a reference. Three breast cancer cell lines, 13 fresh tumor samples, and 6 fine-needle samplings of breast cancer were analyzed using an automated image cytometer. Whenever possible, classic cytogenetics and in situ hybridization on metaphases were performed as controls. Fluorescence ratios representing the imbalances of chromosome 1 arms with values between 1 and 3.2 were measured. Data between classic cytogenetics and interphase cytogenetics were well-correlated (r = 0.89). This method, which enables an easy detection of intrachromosomal imbalances without need of metaphase preparations, detects malignant cells and can be extended to other carcinomas for which chromosome 1 arm imbalances are recurrent or chromosome alterations specific of other malignancies. In comparison to other interphase fluorescence in situ hybridization techniques, it avoids every spot scoring problem encountered when using centromeric probes and the difficulties in interpreting structural rearrangements.