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Both copy number and sequence variations affect expression of human DEFB4

Genes & Immunity volume 11, pages 458–466 (2010)Cite this article

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Abstract

Copy number variations (CNVs) were found to contribute massively to the variability of genomes. One of the best studied CNV region is the β-defensin cluster (DEFB) on 8p23.1. Individual DEFFB copy numbers (CNs) between 2 and 12 were found, whereas low CNs predispose for Crohn's disease. A further level of complexity is represented by sequence variations between copies (multisite variations, MSVs). To address the relation of DEFB CN and MSV to the expression of β-defensin genes, we analyzed DEFB4 expression in B-lymphoblastoid cell lines (LCLs) and primary keratinocytes (normal human epidermal keratinocyte, NHEK) before and after stimulation with lipopolysaccharide, tumor necrosis factor-α (TNF-α) and interferon-γ (IFN-γ). Moreover, we quantified one DEFB4 MSV in DNA and mRNA as a marker for variant-specific expression (VSE) and resequenced a region of ∼2 kb upstream of DEFB4 in LCLs. We found a strong correlation of DEFB CN and DEFB4 expression in 16 LCLs, although several LCLs with very different CNs exhibit similar expression levels. Quantification of the MSV revealed VSE with consistently lower expression of one variant. Costimulation of NHEKs with TNF-α/IFN-γ leads to a synergistic increase in total DEFB4 expression and suppresses VSE. Analysis of the DEFB4 promoter region showed remarkably high density of sequence variabilities (∼1 MSV/41 bp).

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Acknowledgements

The skilful and diligent technical assistance of Beate Szafranski and Ivonne Goerlich is gratefully acknowledged. This work was supported by grants from the Wilhelm Sander Stiftung (2005.045.1) and National Bundesministerium für Bildung und Forschung (01GS0809).

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Authors and Affiliations

  1. Genome Analysis, Leibniz Institute for Age Research—Fritz Lipmann Institute, Jena, Germany

    M Groth, K Szafranski, K Huse, M Kramer & M Platzer

  2. Department of Dermatology, University Medical Center Jena, Jena, Germany

    C Wiegand & J Norgauer

  3. Institute of Clinical Molecular Biology, Christian Albrechts University, Kiel, Germany

    P Rosenstiel & S Schreiber

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  1. M Groth
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Groth, M., Wiegand, C., Szafranski, K. et al. Both copy number and sequence variations affect expression of human DEFB4. Genes Immun 11, 458–466 (2010). https://doi.org/10.1038/gene.2010.19

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