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Using fluorescence in-situ hybridization on interphase chromatin fibers (fiber-FISH), we have constructed an overlapping fiber-FISH contig spanning the non-recombining region of the human Y chromosome (NRY). We first established a standard FISH-signal pattern for a distinct panel of DNA clones on prometaphase Y chromosomes in six healthy fertile men. Clones in the panel were selected from all R-bands as well as deletion intervals 1 through 7 plus PAR1 and PAR2 of the human Y chromosome. We next used signals of these marker clones to build a fiber-FISH contig for the multicopy gene families, CDY, DAZ, RBMY, TSPY and XKRY, along the NRY. Our fiber-FISH contig of human NRY may help to close the four gaps that still exist in the current physical map of the human Y chromosome. Furthermore, it provides a more complete picture with respect to the positions and arrangements of the multicopy gene families along the human NRY.

Applying fluorescence in-situ hybridization (FISH) of various Y chromosomal DNA probes to four familial cases of human Yqs, it was possible to demonstrate that the formation of Yqs must have arisen from a reciprocal translocation involving the short arm of an acrocentric autosome and the heterochromatin of the long arm of the Y chromosome (Yqh). Breakpoints map within Yqh and the proximal short arm of an acrocentric autosome resulting in the gain of a nucleolus organizer region (NOR) including the telomere repeat (TTAGGG)n combined with the loss of the pseudoautosomal region 2 (PAR2) at the long arm of the recipient Y chromosome. In no case could the reciprocal product of an acrocentric autosome with loss of the NOR and gain of PAR2 be detected. Using the 15p-specific classical satellite-III probe D15Z1 in two of the four Yqs probands presented here, it could be shown that the satellited material originated from the short arm of chromosome 15. In contrast to the loss of PAR2 in Yqs chromosomes, another Y chromosomal variant (Yqh-) showing deletion of long-arm heterochromatin in Yq12 has retained PAR2 referring to an interstitial deletion of Yq heterochromatin in such deleted Y chromosomes.

Using fluorescence in-situ hybridization on interphase chromatin fibers (fiber-FISH), we have constructed an overlapping fiber-FISH contig spanning the non-recombining region of the human Y chromosome (NRY). We first established a standard FISH-signal pattern for a distinct panel of DNA clones on prometaphase Y chromosomes in six healthy fertile men. Clones in the panel were selected from all R-bands as well as deletion intervals 1 through 7 plus PAR1 and PAR2 of the human Y chromosome. We next used signals of these marker clones to build a fiber-FISH contig for the multicopy gene families, CDY, DAZ, RBMY, TSPY and XKRY, along the NRY. Our fiber-FISH contig of human NRY may help to close the four gaps that still exist in the current physical map of the human Y chromosome. Furthermore, it provides a more complete picture with respect to the positions and arrangements of the multicopy gene families along the human NRY.

Microdeletions within the AZF (azoospermia factor) a, b and c regions of the Y chromosome can be detected worldwide in 1-10% of infertile men. AZFc, containing genes such as DAZ, CDY, RBMY and others, is most frequently deleted and associated with oligo- or azoospermia. The function of the different genes within AZFc is not yet understood. Here we report the identification and first characterization of the cynomolgus monkey (Macaca fascicularis) homologue of the human CDY gene. cynCDY encodes a 541 aa protein, which like human CDY possesses two putative functional domains: an N-terminal chromodomain, possibly involved in heterochromatin interactions, and a C-terminal domain showing similarity to enoyl-CoA-isomerase, which is involved in fatty acid oxidation. Northern analysis and in-situ hybridization experiments revealed testis- and stage-specific expression of cynCDY mRNA, mainly confined to round and elongating spermatids. Fluorescence in-situ hybridization (FISH) performed on monkey metaphase chromosomes displayed exclusively Y-specific signals in Yq12.1. Using fibre FISH, short signal stretches that indicate the presence of three CDY copies could be visualized, although their integrity or function remains unknown. cynCDY is similar to human CDY with features of a retrotransposon, but different in the 3'UTR. It seems to represent a more ancestral form of CDY and its characterization yields insights into the evolution of candidate genes for AZF.