Analysis of linkage disequilibrium patterns and meiotic crossover distribution in the 206 kb interval surrounding minisatellite MS32 on chromosome 1q42.3

The interstitial minisatellite MS32 is highly variable and is associated with a flanking meiotic recombination hotspot which was the first human hotspot to be characterised at high resolution, using batch sperm typing to recover large numbers of crossover molecules from sperm DNA (Jeffreys, Murray & Neumann, 1998).  This 1.5 kb wide hotspot is similar in morphology to those subsequently defined in the MHC (Jeffreys, Kauppi & Neumann, 2001) and in PAR1 (May et al., 2002) and seems to be responsible for driving tandem repeat DNA instability in the germline within the minisatellite itself.

 

The human genome sequence revealed that minisatellite MS32 resides in an unremarkable region on chromosome 1q42.3 characterised by an average gene density.  This region appears to be more typical of the human genome than either the MHC, which is gene rich and the subject of intense selection, or PAR1 in which male recombination is elevated due to its specialised role in XY pairing.  Minisatellite MS32 is located in a 77 kb long non-coding region between the NID and TM7SF1 genes.

 

To determine patterns of linkage disequilibrium (LD) near MS32, we typed SNPs in a panel of 80 UK semen donors of north European origin across a 206 kb region encompassing the NID gene and the minisatellite and terminating 4.5 kb upstream of TM7SF1.  Regions of LD breakdown were then tested for sperm crossovers.  This analysis demonstrated a pattern of LD and crossover distribution similar to that seen in the MHC, and revealed four new recombination hotspots termed NID1, NID2a, NID2b and NID3 in and near the NID gene, plus three new hotspots (MSTM1a, MSTM1b, MSTM2) between MS32 and the TM7SF1 gene.

 

Data on SNPs and their locations, ASOs used for SNP typing, semen donor genotypes, and procedures for recovering crossover molecules from sperm DNA by single molecule PCR, can be found below:

 

 

 

Annotated sequence around hotspots NID 1-3

showing the location of SNPs and PCR primers used for resequencing, plus approximate position of the centre of each crossover hotspot

 

 

 

Annotated sequence around hotspots MSTM1- 2

showing the location of SNPs and PCR primers used for resequencing, plus approximate position of the centre of each crossover hotspot

 

 

 

Details of each SNP

including location, allele frequencies and the sequences of ASOs used for SNP typing

 

 

 

SNP genotypes

established by genotyping a panel of 80 semen donors

 

 

 

 

SNP haplotypes across MS32 - MSTM2

established by genotyping a panel of 26 semen donors

 

 

 

Sperm crossover analyses at hotspots NID1-3, MSTM1-2

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: 1 September, 2005
Celia A. May
The views expressed in this document are those of the document owner, Alec J. Jeffreys.