Complex evolution of the GSTM gene family involves sharing of GSTM1 deletion polymorphism in humans and chimpanzees View Full Text


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Article Info

DATE

2018-04-25

AUTHORS

M. Saitou, Y. Satta, O. Gokcumen, T. Ishida

ABSTRACT

BACKGROUND: The common deletion of the glutathione S-transferase Mu 1 (GSTM1) gene in humans has been shown to be involved in xenobiotic metabolism and associated with bladder cancer. However, the evolution of this deletion has not been investigated. RESULTS: In this study, we conducted comparative analyses of primate genomes. We demonstrated that the GSTM gene family has evolved through multiple structural variations, involving gene duplications, losses, large inversions and gene conversions. We further showed experimentally that the GSTM1 was polymorphically deleted in both humans and also in chimpanzees, through independent deletion events. To generalize our results, we searched for genic deletions that are polymorphic in both humans and chimpanzees. Consequently, we found only two such deletions among the thousands that we have searched, one of them being the GSTM1 deletion and the other surprisingly being another metabolizing gene, the UGT2B17. CONCLUSIONS: Overall, our results support the emerging notion that metabolizing gene families, such as the GSTM, NAT, UGT and CYP, have been evolving rapidly through gene duplication and deletion events in primates, leading to complex structural variation within and among species with unknown evolutionary consequences. More... »

PAGES

293

References to SciGraph publications

  • 2013-03-07. Rapid birth-and-death evolution of the xenobiotic metabolizing NAT gene family in vertebrates with evidence of adaptive selection in BMC EVOLUTIONARY BIOLOGY
  • 2010-06-20. GSTT1 and GSTM1 gene polymorphisms in European and African populations in MOLECULAR BIOLOGY REPORTS
  • 2011-05-31. Refinement of primate copy number variation hotspots identifies candidate genomic regions evolving under positive selection in GENOME BIOLOGY
  • 2013-02-05. Genome of the Chinese tree shrew in NATURE COMMUNICATIONS
  • 2014-07-20. The Common Marmoset Genome Provides Insight into Primate Biology and Evolution in NATURE GENETICS
  • 2011-01-26. Comparative and demographic analysis of orangutan genomes in NATURE
  • 2014-09-10. Gibbon genome and the fast karyotype evolution of small apes in NATURE
  • 2006-05-17. Genetic evidence for complex speciation of humans and chimpanzees in NATURE
  • 2006-11. Global variation in copy number in the human genome in NATURE
  • 2015-09-30. An integrated map of structural variation in 2,504 human genomes in NATURE
  • 2010-09-15. Molecular evolution and the role of oxidative stress in the expansion and functional diversification of cytosolic glutathione transferases in BMC EVOLUTIONARY BIOLOGY
  • 2012-03-07. Insights into hominid evolution from the gorilla genome sequence in NATURE
  • 2006-06-13. Primate segmental duplications: crucibles of evolution, diversity and disease in NATURE REVIEWS GENETICS
  • 2004-10-19. Genetic polymorphisms of cytochrome P450 2D6 (CYP2D6): clinical consequences, evolutionary aspects and functional diversity in THE PHARMACOGENOMICS JOURNAL
  • 2012-06-13. The bonobo genome compared with the chimpanzee and human genomes in NATURE
  • 2011-03-09. Human-specific loss of regulatory DNA and the evolution of human-specific traits in NATURE
  • 2005-09. Initial sequence of the chimpanzee genome and comparison with the human genome in NATURE
  • 2009-10-07. Origins and functional impact of copy number variation in the human genome in NATURE
  • 2016-12-05. The psoriasis-associated deletion of late cornified envelope genes LCE3B and LCE3C has been maintained under balancing selection since Human Denisovan divergence in BMC EVOLUTIONARY BIOLOGY
  • 2006-03-13. Glutathione S-transferase polymorphisms: cancer incidence and therapy in ONCOGENE
  • 2011-02-13. Discovery and genotyping of genome structural polymorphism by sequencing on a population scale in NATURE GENETICS
  • 2011-02-09. Initial impact of the sequencing of the human genome in NATURE
  • 2010-10-24. A multi-stage genome-wide association study of bladder cancer identifies multiple susceptibility loci in NATURE GENETICS
  • Identifiers

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    http://scigraph.springernature.com/pub.10.1186/s12864-018-4676-z

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