The human Xp/Yp pseudoautosomal region (PAR1): a male recombination "hot" domain

PAR1, the 2.6Mb region at the short ends of the human X and Y chromosomes, plays a very important role in male meiosis; as the largest single region of homology between the X and Y, it is the site of obligatory pairing and exchange between the heterosomes. As a direct consequence of these physical limitations, the whole of PAR1 consitutes a male-specific recombination hot domain at least 20-fold more active than the genome average rate of 0.89cM/Mb.

To complement our recombination studies on the Class II region of the human MHC, we have extended our analysis of the fine-scale distribution of meiotic (sperm) crossovers to the experimentally tractable PAR1. Our initial work has focussed on the SHOX gene region, chosen for the availability of genomic sequence (May et al Nature Genetics 31:272-275 (2002)) SNPs extending over a 43 kb interval, were genotyped by ASO hybridization across a panel of 99 unrelated UK semen donors. In contrast to the MHC, only short domains (~3kb) of strong linkage disequilibrium were found consistent with the region being very active in male recombination. Sperm analysis within a 9.9 kb subregion showed that crossovers cluster into an intense recombination hot spot very similar in morphology to autosomal hot spots. Thus despite the unique standing of PAR1 in male meiosis, general features of the recombination process are similar to those elsewhere in the genome.

Data on the SHOX hotspot can be found below:


Annotated sequence around the SHOX gene

showing the location of SNPs and PCR primers used for resequencing


Details of each SNP

including location, allele frequency in 3 populations and the sequences of ASOs used for SNP typing


SNP genotypes

established by genotyping a panel of North European semen donors, Saami and Vlax Roma


Sperm crossover analysis in the SHOX gene region

with details of allele-specific and universal primers used for recovering crossover molecules from sperm DNA plus information on PCR cycling conditions for each primer combination.


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Last updated: 8 September, 2005
Celia A. May
The views expressed in this document are those of the document owner, Celia A. May.