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Chromosome anomalies/rearrangements of the Y chromosome seldom threaten life and are quite common. The 4.5 Mb AZFc region on Yq11.2 is one of the most polymorphic regions in the human genome. AZFc partial deletion is almost inevitably associated with impaired fertility while the functional significance of AZFc partial duplications remains controversial. In this report, a large Y chromosome with one centromere and two heterochromatic blocks was identified incidentally in two men. The first case was ascertained through surveillance for recurrent miscarriage. The second case was ascertained through amniocytes of a fetus and his father. FISH and array-based comparative genomic hybridization showed duplications of the entire AZFc region as well as Yq euchromatic region. The duplications in Case 1 and Case 2 spanned 4.8 Mb and 6.2 Mb, respectively, of the Yq euchromatic region. These two cases suggest that complete AZFc duplication could be completely benign. It awaits further investigation whether this is a bona fide chromosomal polymorphism.

Overlapping cDNA clones for a novel human X-linked gene, XE169, have been isolated and characterized. The composite cDNA sequence comprises 5910 bp (or 5901 bp) plus a poly(A) tail, with a 531 bp 5' and 696 bp 3' untranslated regions. The sequence represents a full-length or near full-length cDNA for the gene since Northern blot analysis reveals only a single prominent band approximately 6 kb in size. Alternative splicing generates two distinct transcripts either containing or missing a stretch of nine nucleotides in the XE169 single large open reading frame, which in turn predict two XE169 protein isoforms composed of 1557 and 1560 amino acids, respectively. Southern hybridization analysis of a panel of human-mouse somatic cell hybrids containing various portions of translocated human X chromosomes has assigned XE169 to the proximal half of the X short arm between Xp21.1 and the centromere. XE169 is expressed in multiple human tissues tested and homologous sequences exist on the human Y chromosome and in the genomes of five other eutherian mammals examined. RT-PCR analysis of somatic cell hybrids containing either an active or an inactive human X chromosome on a rodent background demonstrated that XE169 escapes X-inactivation.

Among apparently healthy men who nonetheless produce few or no sperm, about ten percent have microdeletions on their Y chromosome. Most of these de novo mutations occur in the AZFc region on the long arm of the chromosome. The high frequency of deletion is explained by the extraordinary structure of the region, which consists almost entirely of very long repeat units.

Mammalian sex chromosomes are divided into sex-specific and pseudoautosomal regions. Sequences in the pseudoautosomal region recombine between the sex chromosomes; the sex-specific sequences normally do not. The interface between sex-specific and pseudoautosomal sequences is the pseudoautosomal boundary. The boundary is the centromeric limit to recombination in the pseudoautosomal region. In man, an Alu repeat element is found inserted at the boundary on the Y chromosome. In the evolutionary comparison conducted here, the Alu repeat element is found at the Y boundary in great apes, but it is not found there in two Old World monkeys. During the evolution of the Old World monkey and great ape lineages, homology between the sex chromosomes was maintained by recombination in the sequences telomeric to the Alu insertion site. The Alu repeat element did not create the present-day boundary; instead, it inserted at the preexisting boundary after the Old World monkey and great ape lineages diverged.