In the past year significant progress has been made in the investigation of the function and transcriptional control of human class I major histocompatibility complex (MHC) receptors expressed on natural killer (NK) cells. We have identified and characterized probabilistic transcriptional switches in the human killer cell immunoglobulin-like receptor (KIR) genes, similar to the switches that we described in the murine Ly49 gene family. A series of genetic polymorphisms have been characterized in the human switch elements, and the functional relevance of these polymorphisms has been demonstrated. This discovery has important implications for the control of stem cell differentiation, and may one day allow us to modify cell fate in differentiating systems such as bone marrow cultures. Our work has defined a novel paradigm for the selective activation of genes, and we are the pioneers in this area. Although the primary mechanism of stochastic decision-making by the KIR/Ly49 probabilistic switches is similar, the mechanism of KIR gene activation/silencing appears to be distinct from the Ly49 system. The KIR switch is positioned adjacent to the coding region, whereas the Ly49 switches are located further upstream. This arrangement leads to the production of double-stranded RNA (dsRNA) in the KIR proximal promoter region if the probabilistic switch is transcribing in the reverse direction, since the antisense transcripts overlap with distal forward KIR transcripts that are present throughout NK development. The possibility that siRNAs could be processed from the dsRNA prompted us to look for small RNAs derived from the KIR dsRNA region. We discovered a 28 base antisense RNA originating from the promoter region with properties similar to the piRNAs that have been associated with gene silencing in germ cells. In collaboration with Dr. Jeff Millers lab at the University of Minnesota, we have demonstrated a central role for the 28 base antisense RNA in KIR gene silencing, using the in vitro NK cell differentiation system developed by Dr. Miller. My group is also investigating polymorphisms in KIR promoter regions that affect either the frequency of NK cells expressing a given gene, or the level of KIR protein expression on the cell surface. Our current work is focussed on a polymorphism in the distal KIR promoter that leads to over-expression of a non-translatable distal transcript, resulting in greatly diminished KIR protein expression. Although we have previously demonstrated an important role for distal transcription in the activation of the proximal KIR promoter, this discovery reveals the potential of distal KIR transcript to interfere with KIR expression when over-expressed. Future plans include: investigation of the mechanism of action of the 28 base RNA;dissecting the role of distal and proximal sense/antisense promoters using BAC transgenes;analysis of KIR promoter polymorphisms and their association with the frequency of gene expression;designing reagents to control KIR gene activation for potential use in the clinic.
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