Single haplotype analysis demonstrates rapid evolution of the killer immunoglobulin-like receptor (KIR) loci in primates

  1. Jennifer G. Sambrook1,
  2. Arman Bashirova2,
  3. Sophie Palmer1,
  4. Sarah Sims1,
  5. John Trowsdale4,
  6. Laurent Abi-Rached5,
  7. Peter Parham5,
  8. Mary Carrington3, and
  9. Stephan Beck1,6
  1. 1 The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kindgom
  2. 2 Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland 21702, USA
  3. 3 Basic Research Program, SAIC-Frederick, Inc., Frederick, Maryland 21702, USA
  4. 4 Immunology Division, Pathology Department, University of Cambridge, Cambridge, CB2 1QP, United Kingdom
  5. 5 Department of Structural Biology, Department of Microbiology, and Department of Immunology, Stanford University School of Medicine, Stanford, California 94305, USA

Abstract

The human killer immunoglobulin-like receptors (KIR) are encoded within the Leukocyte Receptor Complex (LRC) on chromosome 19q13.4. Here we report the comparative genomic analysis of single KIR haplotypes in two other primates. In the common chimpanzee (Pan troglodytes), seven KIR genes (ptKIRnewI, ptKIRnewII, ptKIR2DL5, ptKIRnewIII, ptKIR3DP1, ptKIR2DL4, ptKIR3DL1/2) have been identified, and five KIR genes (mmKIRnewI, mmKIR1D, mmKIR2DL4, mmKIR3DL10, mmKIR3DL1) are present in the haplotype sequenced for the rhesus macaque (Macaca mulatta). Additional cDNA analysis confirms the genes predicted from the genomic sequence and reveals the presence of a fifth novel KIR gene (mmKIRnewII) in the second haplotype of the rhesus macaque. While all known human haplotypes contain both activating and inhibitory KIR genes, only inhibitory KIR genes (characterized by long cytoplasmic tails) were found by in silico and cDNA analyses in the two primate haplotypes studied here. Comparison of the two human and the two non-human primate haplotypes demonstrates rapid diversification of the KIR gene family members, many of which have diverged in a species-specific manner. An analysis of the intronic regions of the two non-human primates reveals the presence of ancient repeat elements, which are indicative of the duplication events that have taken place since the last common ancestor.

Footnotes

  • [The sequence data from this study have been submitted to EMBL/GenBank/DDBJ under accession nos. BX842589–BX842591 and AY728181–AY728190. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: M.B. McChesney.]

  • Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.2381205.

  • ↵6 Corresponding author. E-mail beck{at}sanger.ac.uk; fax 44-(0)1223-494919.

    • Accepted September 14, 2004.
    • Received January 23, 2004.
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  1. doi: 10.1101/gr.2381205 Genome Res. 15: 25-35 Cold Spring Harbor Laboratory Press

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