Molecular analysis of the genomic structure of the human Y chromosome in the euchromatic part of its long arm (Yq11)

Kirsch, Stefan; Keil, Ralph L.; Edelmann, Anke; Henegariu, Octavian; Hirschmann, P.N.; Lepaslier, Denis; Vogt, Peter H.

doi:10.1159/000134481

Cited by 20 publications

(16 citation statements)

References 13 publications

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“…5). Our results do not contradict earlier observations (Archidiacono et al 1998) as YAC clones used for comparative FISH on primate Y chromosomes do not comprise the human Y-chromosomal euchromatin/ heterochromatin transition regions (Affara et al 1996;Kirsch et al 1996). On all higher primate Y chromosomes, the propensity to accumulate SDs in euchromatin/heterochromatin transition regions is clearly visible.…”

Section: Discussionsupporting

confidence: 64%

Evolutionary dynamics of segmental duplications from human Y-chromosomal euchromatin/heterochromatin transition regions

Kirsch¹,

Münch²,

Jiang³

et al. 2008

Genome Res.

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Human chromosomal regions enriched in segmental duplications are subject to extensive genomic reorganization. Such regions are particularly informative for illuminating the evolutionary history of a given chromosome. We have analyzed 866 kb of Y-chromosomal non-palindromic segmental duplications delineating four euchromatin/heterochromatin transition regions (Yp11.2/Yp11.1, Yq11.1/Yq11.21, Yq11.23/Yq12, and Yq12/PAR2). Several computational methods were applied to decipher the segmental duplication architecture and identify the ancestral origin of the 41 different duplicons. Combining computational and comparative FISH analysis, we reconstruct the evolutionary history of these regions. Our analysis indicates a continuous process of transposition of duplicated sequences onto the evolving higher primate Y chromosome, providing unique insights into the development of species-specific Y-chromosomal and autosomal duplicons. Phylogenetic sequence comparisons show that duplicons of the human Yp11.2/Yp11.1 region were already present in the macaque-human ancestor as multiple paralogs located predominantly in subtelomeric regions. In contrast, duplicons from the Yq11.1/Yq11.21, Yq11.23/Yq12, and Yq12/PAR2 regions show no evidence of duplication in rhesus macaque, but map to the pericentromeric regions in chimpanzee and human. This suggests an evolutionary shift in the direction of duplicative transposition events from subtelomeric in Old World monkeys to pericentromeric in the human/ape lineage. Extensive chromosomal relocation of autosomal-duplicated sequences from euchromatin/heterochromatin transition regions to interstitial regions as demonstrated on the pygmy chimpanzee Y chromosome support a model in which substantial reorganization and amplification of duplicated sequences may contribute to speciation.

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Section: Discussionsupporting

confidence: 64%

Evolutionary dynamics of segmental duplications from human Y-chromosomal euchromatin/heterochromatin transition regions

Kirsch¹,

Münch²,

Jiang³

et al. 2008

Genome Res.

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“…It has long been predicted that especially the Y long arm in Yq11 is composed of numerous Y-specific repetitive sequence blocks (Foote et al, 1992;Kirsch et al, 1996). Sequence analysis has now confirmed this assumption.…”

Section: Phvogtmentioning

confidence: 81%

AZF deletions and Y chromosomal haplogroups: history and update based on sequence

Vogt

2005

Human Reproduction Update

121

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AZF deletions are genomic deletions in the euchromatic part of the long arm of the human Y chromosome (Yq11) associated with azoospermia or severe oligozoospermia. Consequently, it can be assumed that these deletions remove Y chromosomal genes required for spermatogenesis. However, these 'classical' or 'complete' AZF deletions, AZFa, AZFb and AZFc, represent only a subset of rearrangements in Yq11. With the benefit of the Y chromosome sequence, more rearrangements (deletions, duplications, inversions) inside and outside the classical AZF deletion intervals have been elucidated and intra-chromosomal non-allelic homologous recombinations (NAHRs) of repetitive sequence blocks have been identified as their major cause. These include duplications in AZFa, AZFb and AZFc and the partial AZFb and AZFc deletions of which some were summarized under the pseudonym 'gr/gr' deletions. At least some of these rearrangements are associated with distinct Y chromosomal haplogroups and are present with similar frequencies in fertile and infertile men. This suggests a functional redundancy of the AZFb/AZFc multi-copy genes. Alternatively, the functional contribution(s) of these genes to human spermatogenesis might be different in men of different Y haplogroups. That raises the question whether, the frequency of Y haplogroups with different AZF gene contents in distinct human populations leads to a male fertility status that varies between populations or whether, the presence of the multiple Y haplogroups implies a balancing selection via genomic deletion/amplification mechanisms.

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“…This susceptibility may be caused by (a) aberrant recombination between areas of homologous or similar sequence repeats between the X and Y chromosomes, (b) aberrant intrachromosomal recombination by unbalanced sister chromatid exchange, or (c) by slippage during DNA replication. Indeed, Kirsch et al [1996] described repetitive-sequence blocks in Yq11 where sister chromatid breakage and inappropriate fusion of broken ends could occur to form dicentric chromosomes. Dicentric Y chromosomes are the most common abnormal Y chromosomes in mosaic UTS patients.…”

Section: Discussionmentioning

confidence: 99%

Identification of high frequency of Y chromosome deletions in patients with sex chromosome mosaicism and correlation with the clinical phenotype and Y‐chromosome instability

Patsalis

Skordis

Sismani

et al. 2005

American J of Med Genetics Pt A

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A mosaic karyotype consisting of a 45,X cell line and a second cell line containing a normal or an abnormal Y chromosome is relatively common and is associated with a wide spectrum of clinical phenotypes. The aim of this study was to investigate patients with such a mosaic karyotype for Y chromosome material loss and then study the possible association of the absence of these regions with the phenotype, diagnosis, and Y-chromosome instability. We studied 17 clinically well-characterized mosaic patients whose karyotype consisted of a 45,X cell line and a second cell line containing a normal or an abnormal Y chromosome. The presence of the Y chromosome centromere was verified by fluorescence in situ hybridization (FISH) and was then characterized by 44 Y-chromosome specific-sequence tagged site (STS) markers. This study identifies a high frequency of Yq chromosome deletions (47%). The deletions extend from interval 5 to 7 sharing a common deleted interval (6F), which overlaps with the azoospermia factor region (AZF) region. This study finds no association between Y-chromosome loci hosting genes other than SRY, and the phenotypic sex, the diagnosis, and the phenotype of the patients. Furthermore, this study shows a possible association of these deletions with Y-chromosome instability.

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Molecular analysis of the genomic structure of the human Y chromosome in the euchromatic part of its long arm (Yq11)

Cited by 20 publications

References 13 publications

Evolutionary dynamics of segmental duplications from human Y-chromosomal euchromatin/heterochromatin transition regions

Evolutionary dynamics of segmental duplications from human Y-chromosomal euchromatin/heterochromatin transition regions

AZF deletions and Y chromosomal haplogroups: history and update based on sequence

Identification of high frequency of Y chromosome deletions in patients with sex chromosome mosaicism and correlation with the clinical phenotype and Y‐chromosome instability

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