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Characterization of a weakly expressed KIR2DL1 variant reveals a novel upstream promoter that controls KIR expression

Genes & Immunity volume 15, pages 440–448 (2014)Cite this article

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Abstract

Members of the human KIR (killer cell immunoglobulin-like receptor) class I major histocompatibility complex receptor gene family contain multiple promoters that determine the variegated expression of KIR on natural killer cells. In order to identify novel genetic alterations associated with decreased KIR expression, a group of donors was characterized for KIR gene content, transcripts and protein expression. An individual with a single copy of the KIR2DL1 gene but a very low level of gene expression was identified. The low expression phenotype was associated with a single-nucleotide polymorphism (SNP) that created a binding site for the inhibitory ZEB1 (Zinc finger E-box-binding homeobox 1) transcription factor adjacent to a c-Myc binding site previously implicated in distal promoter activity. Individuals possessing this SNP had a substantial decrease in distal KIR2DL1 transcripts initiating from a novel intermediate promoter located 230 bp upstream of the proximal promoter start site. Surprisingly, there was no decrease in transcription from the KIR2DL1 proximal promoter. Reduced intermediate promoter activity revealed the existence of alternatively spliced KIR2DL1 transcripts containing premature termination codons that initiated from the proximal KIR2DL1 promoter. Altogether, these results indicate that distal transcripts are necessary for KIR2DL1 protein expression and are required for proper processing of sense transcripts from the bidirectional proximal promoter.

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Acknowledgements

This project has been funded in whole or in part with federal funds from the National Cancer Institute (NCI), NIH, under contract HHSN261200800001E and NCI grant P01 111412 (to JSM and SKA). This research was supported in part by the Intramural Research Program of the NIH, NCI, Center for Cancer Research. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products or organizations imply endorsement by the US Government.

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  1. P W Wright, H Li and A Huehn: The first three authors contributed equally to this work.

Authors and Affiliations

  1. Basic Science Program, Leidos Biomedical Research Inc., Lab of Experimental Immunology, Frederick National Lab, Frederick, MD, USA

    P W Wright, H Li & S K Anderson

  2. Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA

    A Huehn, G M O'Connor & S K Anderson

  3. Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN, USA

    S Cooley & J S Miller

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  1. P W Wright
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  2. H Li
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  4. G M O'Connor
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  5. S Cooley
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  6. J S Miller
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  7. S K Anderson
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Correspondence to S K Anderson.

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Wright, P., Li, H., Huehn, A. et al. Characterization of a weakly expressed KIR2DL1 variant reveals a novel upstream promoter that controls KIR expression. Genes Immun 15, 440–448 (2014). https://doi.org/10.1038/gene.2014.34

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  • DOI: https://doi.org/10.1038/gene.2014.34

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