Genetic Recombination Is Targeted towards Gene Promoter Regions in Dogs

Adam Auton, Ying Rui Li, Jeffrey Kidd, Kyle Oliveira, Julie Nadel, J. Kim Holloway, Jessica J. Hayward, Paula E. Cohen, John M. Greally, Jun Wang, Carlos D. Bustamante, Adam R. Boyko

Research output: Contribution to journalArticle

93 Citations (Scopus)

Abstract

The identification of the H3K4 trimethylase, PRDM9, as the gene responsible for recombination hotspot localization has provided considerable insight into the mechanisms by which recombination is initiated in mammals. However, uniquely amongst mammals, canids appear to lack a functional version of PRDM9 and may therefore provide a model for understanding recombination that occurs in the absence of PRDM9, and thus how PRDM9 functions to shape the recombination landscape. We have constructed a fine-scale genetic map from patterns of linkage disequilibrium assessed using high-throughput sequence data from 51 free-ranging dogs, Canis lupus familiaris. While broad-scale properties of recombination appear similar to other mammalian species, our fine-scale estimates indicate that canine highly elevated recombination rates are observed in the vicinity of CpG rich regions including gene promoter regions, but show little association with H3K4 trimethylation marks identified in spermatocytes. By comparison to genomic data from the Andean fox, Lycalopex culpaeus, we show that biased gene conversion is a plausible mechanism by which the high CpG content of the dog genome could have occurred.

Original languageEnglish (US)
Article numbere1003984
JournalPLoS Genetics
Volume9
Issue number12
DOIs
StatePublished - 2013

Fingerprint

genetic recombination
Genetic Promoter Regions
Genetic Recombination
recombination
promoter regions
Dogs
gene
dogs
mammals
Genes
gene conversion
genes
Canidae
Canis lupus
spermatocytes
linkage disequilibrium
foxes
Mammals
mammal
canid

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Ecology, Evolution, Behavior and Systematics
  • Cancer Research
  • Genetics(clinical)

Cite this

Auton, A., Rui Li, Y., Kidd, J., Oliveira, K., Nadel, J., Holloway, J. K., ... Boyko, A. R. (2013). Genetic Recombination Is Targeted towards Gene Promoter Regions in Dogs. PLoS Genetics, 9(12), [e1003984]. https://doi.org/10.1371/journal.pgen.1003984

Genetic Recombination Is Targeted towards Gene Promoter Regions in Dogs. / Auton, Adam; Rui Li, Ying; Kidd, Jeffrey; Oliveira, Kyle; Nadel, Julie; Holloway, J. Kim; Hayward, Jessica J.; Cohen, Paula E.; Greally, John M.; Wang, Jun; Bustamante, Carlos D.; Boyko, Adam R.

In: PLoS Genetics, Vol. 9, No. 12, e1003984, 2013.

Research output: Contribution to journalArticle

Auton, A, Rui Li, Y, Kidd, J, Oliveira, K, Nadel, J, Holloway, JK, Hayward, JJ, Cohen, PE, Greally, JM, Wang, J, Bustamante, CD & Boyko, AR 2013, 'Genetic Recombination Is Targeted towards Gene Promoter Regions in Dogs', PLoS Genetics, vol. 9, no. 12, e1003984. https://doi.org/10.1371/journal.pgen.1003984
Auton A, Rui Li Y, Kidd J, Oliveira K, Nadel J, Holloway JK et al. Genetic Recombination Is Targeted towards Gene Promoter Regions in Dogs. PLoS Genetics. 2013;9(12). e1003984. https://doi.org/10.1371/journal.pgen.1003984
Auton, Adam ; Rui Li, Ying ; Kidd, Jeffrey ; Oliveira, Kyle ; Nadel, Julie ; Holloway, J. Kim ; Hayward, Jessica J. ; Cohen, Paula E. ; Greally, John M. ; Wang, Jun ; Bustamante, Carlos D. ; Boyko, Adam R. / Genetic Recombination Is Targeted towards Gene Promoter Regions in Dogs. In: PLoS Genetics. 2013 ; Vol. 9, No. 12.
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