Fine-scale maps of recombination rates and hotspots in the mouse genome

Hadassa Brunschwig, Liat Levi, Eyal Ben-David, Robert Williams, Benjamin Yakir, Sagiv Shifman

Research output: Contribution to journalArticle

47 Citations (Scopus)

Abstract

Recombination events are not uniformly distributed and often cluster in narrow regions known as recombination hotspots. Several studies using different approaches have dramatically advanced our understanding of recombination hotspot regulation. Population genetic data have been used to map and quantify hotspots in the human genome. Genetic variation in recombination rates and hotspots usage have been explored in human pedigrees, mouse intercrosses, and by sperm typing. These studies pointed to the central role of the PRDM9 gene in hotspot modulation. In this study, we used single nucleotide polymorphisms (SNPs) from wholegenome resequencing and genotyping studies of mouse inbred strains to estimate recombination rates across the mouse genome and identified 47,068 historical hotspots-an average of over 2477 per chromosome. We show by simulation that inbred mouse strains can be used to identify positions of historical hotspots. Recombination hotspots were found to be enriched for the predicted binding sequences for different alleles of the PRDM9 protein. Recombination rates were on average lower near transcription start sites (TSS). Comparing the inferred historical recombination hotspots with the recent genome-wide mapping of double-strand breaks (DSBs) in mouse sperm revealed a significant overlap, especially toward the telomeres. Our results suggest that inbred strains can be used to characterize and study the dynamics of historical recombination hotspots. They also strengthen previous findings on mouse recombination hotspots, and specifically the impact of sequence variants in Prdm9.

Original languageEnglish (US)
Pages (from-to)757-764
Number of pages8
JournalGenetics
Volume191
Issue number3
DOIs
StatePublished - Jul 1 2012

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Genetic Recombination
Genome
Inbred Strains Mice
Spermatozoa
Chromosome Mapping
Transcription Initiation Site
Telomere
Population Genetics
Human Genome
Pedigree
Single Nucleotide Polymorphism
Chromosomes
Alleles

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Brunschwig, H., Levi, L., Ben-David, E., Williams, R., Yakir, B., & Shifman, S. (2012). Fine-scale maps of recombination rates and hotspots in the mouse genome. Genetics, 191(3), 757-764. https://doi.org/10.1534/genetics.112.141036

Fine-scale maps of recombination rates and hotspots in the mouse genome. / Brunschwig, Hadassa; Levi, Liat; Ben-David, Eyal; Williams, Robert; Yakir, Benjamin; Shifman, Sagiv.

In: Genetics, Vol. 191, No. 3, 01.07.2012, p. 757-764.

Research output: Contribution to journalArticle

Brunschwig, H, Levi, L, Ben-David, E, Williams, R, Yakir, B & Shifman, S 2012, 'Fine-scale maps of recombination rates and hotspots in the mouse genome', Genetics, vol. 191, no. 3, pp. 757-764. https://doi.org/10.1534/genetics.112.141036
Brunschwig, Hadassa ; Levi, Liat ; Ben-David, Eyal ; Williams, Robert ; Yakir, Benjamin ; Shifman, Sagiv. / Fine-scale maps of recombination rates and hotspots in the mouse genome. In: Genetics. 2012 ; Vol. 191, No. 3. pp. 757-764.
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