MSY Breakpoint Mapper, a database of sequence-tagged sites useful in defining naturally occurring deletions in the human Y chromosome

Y chromosome deletions arise frequently in human populations, where they cause sex reversal and Turner syndrome and predispose individuals to infertility and germ cell cancer. Knowledge of the nucleotide sequence of the male-specific region of the Y chromosome (MSY) makes it possible to precisely demarcate such deletions and the repertoires of genes lost, offering insights into mechanisms of deletion and the molecular etiologies of associated phenotypes. Such deletion mapping is usually conducted using polymerase chain reaction (PCR) assays for the presence or absence of a series of Y-chromosomal DNA markers, or sequence-tagged sites (STSs). In the course of mapping intact and aberrant Y chromosomes during the past two decades, we and our colleagues have developed robust PCR assays for 1287 Y-specific STSs. These PCR assays amplify 1698 loci at an average spacing of <14 kb across the MSY euchromatin. To facilitate mapping of deletions, we have compiled a database of these STSs, MSY Breakpoint Mapper (http://breakpointmapper.wi.mit.edu/). When queried, this online database provides regionally targeted catalogs of STSs and nearby genes. MSY Breakpoint Mapper is useful for efficiently and systematically defining the breakpoint(s) of virtually any naturally occurring Y chromosome deletion.National Institutes of Health (U.S.)Howard Hughes Medical Institut

Diverse outcomes of homologous recombination in the human Y chromosome

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2008.Includes bibliographical references.Mammalian sex chromosomes began diverging from an ordinary pair of autosomes roughly 300 million years ago. Inversions in the evolving Y chromosome sequentially suppressed recombination with the X chromosome. While pseudoautosomal regions in the human Y chromosome still participate regularly in allelic homologous recombination, the male-specific region of the Y (MSY) - the only haploid portion of the nuclear genome - does not. It does, however, engage in non-allelic homologous recombination. In this thesis, I examine modes and outcomes of non-allelic homologous recombination in the MSY. The predictions presented here are based on the double-strand break repair model of recombination between homologous chromosomes, in which a double-strand break (DSB) is the common precursor to crossing over and gene conversion. First, I show that massive MSY-specific palindromes, which maintain arm-to-arm sequence identity via gene conversion, are also the targets of crossing over. Crossover events in palindromes can lead to isochromosome formation and diverse reproductive disorders including sex reversal, male infertility, and Turner syndrome. Second, I demonstrate that a region of the MSY - thought to be recombinationally suppressed with the X chromosome - does undergo extensive X-Y gene conversion. This region encompasses hotspots of ectopic crossover events that lead to X-Y translocations associated with sex reversal syndromes. Although sequences in the MSY engage in productive recombination via gene conversion, alternative resolution of DSBs by crossing over can produce evolutionary "dead ends".by Julian H. Lange.Ph.D

Case of Inherited Partial AZFa Deletion without Impact on Male Fertility

Male factor infertility accounts for 40–50% of all infertility cases. Deletions of one or more AZF region parts in chromosome Y are one of the most common genetic causes of male infertility. Usually full or partial AZF deletions, including genes involved in spermatogenesis, are associated with spermatogenic failure. Here we report a case of a Caucasian man with partial AZFa region deletion from a couple with secondary infertility. Partial AZFa deletion, involving part of USP9Y gene appears to be benign, as we proved transmission from father to son. According to our results, it is recommended to revise guidelines on markers selected for testing of AZFa region deletion, to be more selective against DDX3Y gene and exclude probably benign microdeletions involving only USP9Y gene.publishersversionPeer reviewe

Intrachromosomal homologous recombination between inverted amplicons on opposing Y-chromosome arms

Amplicons – large, nearly identical repeats in direct or inverted orientation – are abundant in the male-specific region of the human Y chromosome (MSY) and provide targets for intrachromosomal non-allelic homologous recombination (NAHR). Thus far, NAHR events resulting in deletions, duplications, inversions, or isodicentric chromosomes have been reported only for amplicon pairs located exclusively on the short arm (Yp) or the long arm (Yq). Here we report our finding of four men with Y chromosomes that evidently formed by intrachromosomal NAHR between inverted repeat pairs comprising one amplicon on Yp and one amplicon on Yq. In two men with spermatogenic failure, sister-chromatid crossing-over resulted in pseudoisoYp chromosome formation and loss of distal Yq. In two men with normal spermatogenesis, intrachromatid crossing-over generated pericentric inversions. These findings highlight the recombinogenic nature of the MSY, as intrachromosomal NAHR occurs for nearly all Y-chromosome amplicon pairs, even those located on opposing chromosome arms.National Institutes of Health (U.S.)Netherlands Organization for Scientific ResearchAcademic Medical Center (University of Amsterdam

Isodicentric Y Chromosomes and Sex Disorders as Byproducts of Homologous Recombination that Maintains Palindromes

Massive palindromes in the human Y chromosome harbor mirror-image gene pairs essential for spermatogenesis. During evolution, these gene pairs have been maintained by intrapalindrome, arm-to-arm recombination. The mechanism of intrapalindrome recombination and risk of harmful effects are unknown. We report 51 patients with isodicentric Y (idicY) chromosomes formed by homologous crossing over between opposing arms of palindromes on sister chromatids. These ectopic recombination events occur at nearly all Y-linked palindromes. Based on our findings, we propose that intrapalindrome sequence identity is maintained via noncrossover pathways of homologous recombination. DNA double-strand breaks that initiate these pathways can be alternatively resolved by crossing over between sister chromatids to form idicY chromosomes, with clinical consequences ranging from spermatogenic failure to sex reversal and Turner syndrome. Our observations imply that crossover and noncrossover pathways are active in nearly all Y-linked palindromes, exposing an Achilles' heel in the mechanism that preserves palindrome-borne genes.National Institutes of Health (U.S.)Howard Hughes Medical InstituteNetherlands Organization for Scientific ResearchUniversity of Amsterdam. Academic Medical CenterBoehringer Ingelheim (Fellowship

Y is Male Breast Cancer so Rare?

Male breast cancer (MBC) occurs at less than 1% frequency of female breast cancer, and its actual etiology is still unclear. We hypothesize that males are protected from contracting breast cancer because the male-specific region of the human Y chromosome (MSY) has breast tumor suppressive function. Here, we show via fluorescence in situ hybridization (FISH) and droplet digital PCR (ddPCR) that Y chromosome was lost clonally at a frequency of ~15% (5/32) in two independently collated cohorts of MBC patients. We also show via FISH that this clonal Y loss occurred since ductal carcinoma in situ (DCIS) stage of MBC. Furthermore, we investigated regional loss of the Y chromosome in MBC patients who retained their Y chromosomes with STS-PCR (sequence-tagged-site PCR), derived from the male specific region of the Y chromosome Breakpoint Mapper (MSY-BPM), and showed nullisomic loss of TMSB4Y in a MBC patient. We showed via immunohistochemistry (IHC) that TMSB4Y is expressed in normal male breast tissue. Dox inducible cell lines of TMSB4Y, TmY1 and TmY2, were generated in the female breast epithelial cell line MCF-10A background. Dox-induced expression of TMSB4Y resulted in altered morphology and reduced cell proliferation. Furthermore, reverse phase protein array (RPPA) analysis on TmY1 showed reduced expression of Syk (spleen tyrosine kinase) after Dox-induced expression of TMSB4Y. Interestingly, though TMSB4Y is highly homologous to its homologue TMSB4X on the X chromosome, the TMSB4Y antibody is solely specific to TMSB4Y, which suggests differences between TMSB4Y and TMSB4X. Taken together, our results suggest that in situ clonal loss of human Y chromosome might contribute to MBC tumorigenesis, and that TMSB4Y is tumor suppressive through regulating breast cell morphology and reducing cell proliferation

TMSB4Y is a Candidate Tumor Suppressor on the Y Chromosome and is Deleted in Male Breast Cancer.

Male breast cancer comprises less than 1% of breast cancer diagnoses. Although estrogen exposure has been causally linked to the development of female breast cancers, the etiology of male breast cancer is unclear. Here, we show via fluorescence in situ hybridization (FISH) and droplet digital PCR (ddPCR) that the Y chromosome was clonally lost at a frequency of ~16% (5/31) in two independent cohorts of male breast cancer patients. We also show somatic loss of the Y chromosome gene TMSB4Y in a male breast tumor, confirming prior reports of loss at this locus in male breast cancers. To further understand the function of TMSB4Y, we created inducible cell lines of TMSB4Y in the female human breast epithelial cell line MCF-10A. Expression of TMSB4Y resulted in aberrant cellular morphology and reduced cell proliferation, with a corresponding reduction in the fraction of metaphase cells. We further show that TMSB4Y interacts directly with β-actin, the main component of the actin cytoskeleton and a cell cycle modulator. Taken together, our results suggest that clonal loss of the Y chromosome may contribute to male breast carcinogenesis, and that the TMSB4Y gene has tumor suppressor properties

Caracterización de polimorfismos genéticos en la región AZF del cromosoma Y potencialmente asociados a infertilidad en distintos grupos étnicos de la población argentina actual

Microdeletions in the AZF region of the Y chromosome are routinely analyzed in azoospermic and severe oligozoospermic patients, in order to predict sperm recovery by testicular biopsies. Several population studies have shown variation in the prevalence and effect of these microdeletions. Aiming to characterize the Argentinean population, 240 fertile men belonging to haplogroup Q3, 170 infertile and 90 azoospermic patients have been analyzed. Our results discarded the existence of constitutive microdeletions in haplogroup Q3, as well as the association between partial deletions and sperm count decrease. The prevalence of complete microdeletions was 11.1%, being only correlated with severe sperm count alterations, regardless of the patient?s haplogroup. Conversely, certain haplogroups showed association with partial deletions without any pathogenic effect. Only deletions of AZFbc and AZFabc regions evidenced complete absence of spermatogenesis in the testis. The existence of azoospermic patients without microdeletions suggests that other factors could be affecting spermatogenesis. Given that it is not possible to predict sperm recovery by analyzing only the currently suggested markers, the present work concluded with the development of a molecular biology tool for the detection of spermatogenesis candidate genes. The identification of novel markers will allow a better diagnosis and genetic counselling for the infertile couple.Fil: Alechine, Evguenia. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Servicio de Huellas Digitales Genéticas; ArgentinaEl estudio de microdeleciones en la región AZF del cromosoma Y se solicita de rutina a pacientes azoospérmicos u oligozoospérmicos severos, para predecir la recuperación de espermatozoides mediante biopsia testicular. En distintas poblaciones se ha demostrado variación en la prevalencia y efecto de estas microdeleciones. Con el objetivo de estudiar a la población argentina, se analizaron 240 hombres fértiles del haplogrupo Q3, 170 pacientes infértiles y 90 azoospérmicos. A partir de los resultados obtenidos, se descartaron deleciones constitutivas en el haplogrupo Q3, así como la asociación entre deleciones parciales y disminución del recuento espermático. Se observó una prevalencia del 11,1% de microdeleciones completas que se correlacionaron con alteraciones severas del recuento espermático, independientemente del haplogrupo del paciente. Sin embargo, las deleciones parciales se correlacionaron con determinados haplogrupos sin efecto patogénico. Únicamente las deleciones AZFbc y AZFabc presentaron ausencia de espermatozoides a nivel testicular. La existencia de pacientes azoospérmicos sin deleciones indicaría que existen otros factores que afectan la espermatogénesis. Dado que no es posible predecir la recuperación de espermatozoides empleando únicamente los marcadores recomendados, el presente trabajo culminó con el desarrollo de una herramienta para la detección de genes candidatos de la espermatogénesis. La identificación de nuevos marcadores permitirá tomar decisiones clínicas apropiadas y asesorar genéticamente a la pareja infértil