p49f, a highly polymorphic probe, that detects Taq1 RFLPs on the human Y chromosome

Lucotte, G.; Ngo, Ngan

doi:10.1093/nar/13.22.8285

Cited by 54 publications

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“…The third polymorphic AZF-locus (DYS1; 49f probe; Lucotte and Ngo, 1985) is composed of 18 Taq I restricted genomic Y-DNA fragments (A -R; Figure 2) and part of the DAZ gene structure in AZFc ( Figure 3A). The variability of six Taq I fragments (A, C, D, F and I: present or absent; A and D modified in length: A1 ¼ 11.1 kb; A2 ¼ 14.8 kb; A3 ¼ 17.3 kb; A4 ¼ 19.6 kb; D1 ¼ 7.2 kb; D2 ¼ 6.9 kb) seemed to occur independently from each other and therefore established the first multi-allelic Y chromosome marker system (Ngo et al, 1986).…”

Section: Polymorphic Y-fragments In Azf Regions Establish First Y Chrmentioning

confidence: 99%

“…The DYS1 length variabilities are reflecting the variable number and sequence variants of the repetitive exon 7 copies in the four DAZ genes (also called DAZ-repeats) to which the 49f probe cross hybridised; the cross hybridising K and L female fragments belong to the autosomal DAZL gene copy on the short arm of chromosome 3 (Saxena et al, 1996; Vogt et al, 1997). The first genomic sequence variants in the three AZF intervals were detected by DNA blot hybridisation with the probes 12f2 (Casanova et al, 1985), 50f2 (Disteche et al, 1986) and 49f (Lucotte and Ngo, 1985), respectively. The restriction enzymes used to identify the variants are given at the bottom of the blot pictures.…”

Section: Polymorphic Y-fragments In Azf Regions Establish First Y Chrmentioning

confidence: 99%

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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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Section: Polymorphic Y-fragments In Azf Regions Establish First Y Chrmentioning

confidence: 99%

Section: Polymorphic Y-fragments In Azf Regions Establish First Y Chrmentioning

confidence: 99%

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

Vogt

2005

Human Reproduction Update

121

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“…As a result, it would be expected that much of the Y chromosomal sequence would be maintained among the higher primates. In population genetic studies of humans, more polymorphic markers have been described for the pseudoautosomal than in the sex-specific region (Page et al 1982;Lucotte and Ngo 1985;Casanova et al 1985;Ngo et al 1986;Jakubiczka et al 1989). A Y-linked rate of nucleotide substitution ("mol- …”

Section: Discussionmentioning

confidence: 99%

Conservation of human Y chromosome sequences among male great apes: Implications for the evolution of Y chromosomes

Allen

Ostrer

1994

J Mol Evol

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Nine newly described single-copy and low-copy-number genomic DNA sequences isolated from a flow-sorted human Y chromosome library were mapped to regions of the human Y chromosome and were hybridized to Southern blots of male and female great ape genomic DNAs (Gorilla gorilla, Pan troglodytes, Pongo pygmaeus). Eight of the nine sequences mapped to the euchromatic Y long arm (Yq) in humans, and the ninth mapped to the short arm or pericentromeric region. All nine of the newly identified sequences and two additional human Yq sequences hybridized to restriction fragments in male but not female genomic DNA from the great apes, indicating Y chromosome localization. Seven of these 11 human Yq sequences hybridized to similarly-sized restriction endonuclease fragments in all the great ape species analyzed. The five human sequences that mapped to the most distal subregion of Yq (deletion of which region is associated with spermatogenic failure in humans) were hybridized to Southern blots generated by pulsed-field gel electrophoresis. These sequences define a region of approximately 1 Mb on human Yq in which HpaII tiny fragment (HTF) islands appear to be absent. The conservation of these human Yq sequences on great ape Y chromosomes indicates a greater stability in this region of the Y than has been previously described for most anonymous human Y chromosomal sequences. The stability of these sequences on great ape Y chromosomes seems remarkable given that this region of the Y does not undergo meiotic recombination and the sequences do not appear to encode genes for which positive selection might occur.

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“…The p49a)flTaqI Y-specific polymorphism (locus DYS1) was described initially by Lucotte and Ngo (1985) and more fully by . These two probes are subfragnients, 6 kb apart, of the Y-49 sequence, a human Y-chromosome-enriched cosmid library (Bishop et al, 1984)) and have been mapped to Yq11.2 (Quack et al, 1988).…”

Section: P49dp49f (Hgm Locus Dys 7)mentioning

confidence: 99%

“…Some fragments can be either present or absent whereas other fragments, such as A and D, can show size variations and can be present or absent. This fragment variability was initially explained by point mutations within the TaqI sites, since RFLPs were not detected with other enzymes (Lucotte and Ngo, 1985;. The different fragments were considered an "allelic series" (because each male exhibited only one pattern type for each of the variable fragments), and because of the haploid status of the Y chromosome, the combined pattern of the series was referred to as the "p49 haplotype" or 'Y-specific haplotype.…”

Section: P49dp49f (Hgm Locus Dys 7)mentioning

confidence: 99%

Y-chromosome-specific restriction fragment length polymorphisms (RFLPs): Relevance to human evolution and human variation

Mitchell

1996

Am. J. Hum. Biol.

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The human Y chromosome comprises two distinct parts: the pseudoautosomal region on the tip of the short arm that pairs with the X chromosome in male meiosis and undergoes recombination, and the remainder of the chromosome, which is male‐specific and not involved in recombination. It is this haploid part of the Y chromosome, with its accumulation of mutations, that is of interest to human biologists because the variation within it potentially reflects the paternal line in human evolution (just as mtDNA analysis represents maternal lineages). The Y chromosome, however, appears to contain very few restriction fragment length polymorphisms (RFLPs), and furthermore, understanding of the polymorphic basis of some of these is presently imperfect. These latter problems include the possibility of multiple origins of the same allele, especially in repeat sequence polymorphisms, and failure to recognize the ancestral allele at a locus. All of these restrictions and difficulties mean that no comprehensive understanding of either Y chromosome evolution or its variability among the world's populations is yet possible. This report examines the current knowledge of Y‐chromosome population genetics obtained using probes such as p12f, p49a, pYAP, and pYαl, including their use in measuring gene flow and also in population histories and differentiation. Most studies have reported allele frequencies at a particular locus, but a fuller understanding of Y chromosome evolution and variation will require haplotype data. One interesting observation is the low diversity for some Y‐chromosome polymorphisms in African populations compared to Caucasoids, a contrast to the pattern seen for other DNA polymorphisms. The role of different mate choice systems in acting to substantially reduce Y‐chromosome variation is considered. © 1996 Wiley‐Liss, Inc.

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p49f, a highly polymorphic probe, that detects Taq1 RFLPs on the human Y chromosome

Cited by 54 publications

References 0 publications

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

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

Conservation of human Y chromosome sequences among male great apes: Implications for the evolution of Y chromosomes

Y-chromosome-specific restriction fragment length polymorphisms (RFLPs): Relevance to human evolution and human variation

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