Two long homologous retroviral sequence blocks in proximal Yq11 cause AZFa microdeletions as a result of intrachromosomal recombination events

Abstract

We mapped the breakpoints of the AZoospermia factor a (AZFa) microdeletion located in proximal Yq11 in six men with complete germ cell aplasia, i.e. Sertoli Cell Only syndrome (SCO). The proximal breakpoints were identified in a long retroviral sequence block (HERV15yq1: 9747 nucleotides) at the 5' end of the DYS11 DNA locus in Yq11, interval D3. The distal breakpoints were found in a homologous HERV15 sequence block mapped to the Yq11 interval D6, i.e. in the distal part of the AZFa region (HERV15yq2: 9969 nucleotides). Compared with the HERV15yq1 sequence, HERV15yq2 is marked by a deletion of a HERV15 sequence domain at its 5' end and insertion of an LINE 1 3'-UTR sequence block (L1PA4) of similar length at its 3' end. The deletion of the L1PA4 element was recognized as the molecular origin of the DYS11 12f2 restriction fragment length polymorphism. For all six AZFa patients it was possible to perform PCR experiments bridging both retroviral sequence blocks, which map in a distance of 781.557 kb in proximal Yq11 in fertile men. The AZFa breakpoint-fusion regions were located in their recombined HERV15yq1/HERV15yq2 sequence blocks in either one of two long identical sequence domains (ID1 and ID2). We therefore assume that intrachromosomal recombination events between the two homologous retroviral sequence blocks in proximal Yq11 are probably the causative agents for most of the AZFa microdeletions observed in men with SCO syndrome. A mean value of 792 kb was estimated for their molecular lengths.

The Y chromosome-linked copy number variations and male fertility

“…Complete AZFa deletions occurs after homologous recombination between identical sequence blocks within the retroviral sequences in the same orientation HERVyq1 and HERVyq2 (9)(10)(11). The complete deletion of AZFb is caused by homologous recombination between the palindromes P5/proximal P1 which removes also part of the AZFc region belonging to P1 (8).…”

Homozygous deletion of DIS3L2 exon 9 due to non-allelic homologous recombination between LINE-1s in a Japanese patient with Perlman syndrome

“…6 Although Alu-mediated NAHR contributes to a large variety of genetic disorders, L1-mediated NAHR and human endogenous retrovirus-mediated NAHR are very rare causes of human diseases. [9][10][11][12] Only three human diseasesglycogen storage disease type IXb, Alport syndrome-diffuse leiomyomatosis, and Ellis-van Creveld syndrome -have been reported to be caused by L1-mediated NAHR. [13][14][15] To our knowledge, this is the fourth NAHR event to cause human disease, in this case Perlman syndrome.…”

Human Y Chromosome and Male Infertility: Forward and Back from Azoospermia Factor Chromatin Structure to Azoospermia Factor Gene Function

“…An intrachromosomal recombination event between 2 homologous retroviral sequence blocks (HERV15yq1 and HERV15yq2) deletes 792 kb of this AZFa region [47][48][49] . No somatic pathology was observed in men with this large Y deletion; however, they had a severe testicular pathology.…”