A Sequence-Ready Physical Map of the Region Containing the Human Natural Killer Gene Complex on Chromosome 12p12.3–p13.2

Abstract

We developed a sequence-ready physical map of a part of human chromosome 12p12.3–p13.2 where the natural killer gene complex (NKC) is located. The NKC includes a cluster of genes with structure similar to that of the Ca2+-dependent lectin superfamily of glycoproteins that are expressed on the surface of most natural killer (NK) cells and a subset of T cells. These killer cell lectin-like receptors (KLR) are involved in NK target cell recognition, leading to activation or inhibition of NK cell function. We used a number of sequence-tagged site (STS) markers from this region to screen two large insert bacterial artificial chromosome (BAC) libraries and a bacteriophage P1-derived (PAC) chromosome library. The clones were assembled into contiguous sets by STS content analysis. The 72-BAC and 11-PAC contig covers nearly 2 Mb of DNA and provides an average marker resolution of 26 kb. We have precisely localized 17 genes, 5 expressed sequence tags, and 49 STSs within this contig. Of this total number of STS, 30 are newly developed by clone-end sequencing. We established the order of the genes as tel–M6PR–MAFAL (HGMW-approved symbol KLRG1)–A2M–PZP–A2MP–NKRP1A (HGMW-approved symbol KLRB1)–CD69–AICL (HGMW-approved symbol CLECSF2)–KLRF1–OLR1–CD94 (HGMW-approved symbol KLRD1)–NKG2D (HGMW-approved symbol D12S2489E)–PGFL–NKG2F (HGMW-approved symbol KLRC4)–NKG2E (HGMW-approved symbol KLRC3)–NKG2A (HGMW-approved symbol KLRC1)–LY49L (HGMW-approved symbol KLRA1)–cen. This map would facilitate the cloning of new KLR genes and the complete sequencing of this region.