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Both copy number and sequence variations affect expression of human DEFB4
M Groth1, C Wiegand, K Szafranski
1Genome Analysis, Leibniz Institute for Age Research-Fritz Lipmann Institute, Jena, Germany. mgroth@fli-leibniz.de
Genes and Immunity
|May 7, 2010
Summary
Copy number variations (CNVs) in the beta-defensin cluster (DEFB) impact gene expression. We found that DEFB copy number and specific sequence variations influence DEFB4 expression levels in cells and skin, with implications for immune response.
Area of Science:
- Genomics
- Immunology
- Molecular Biology
Background:
- Copy number variations (CNVs) significantly contribute to genomic variability.
- The beta-defensin cluster (DEFB) on chromosome 8p23.1 is a well-studied CNV region, with copy numbers ranging from 2 to 12.
- Low DEFB copy numbers are associated with an increased predisposition to Crohn's disease.
Purpose of the Study:
- To investigate the relationship between DEFB copy number (CN) and multisite variations (MSVs) and the expression of beta-defensin genes.
- To analyze DEFB4 expression in B-lymphoblastoid cell lines (LCLs) and normal human epidermal keratinocytes (NHEKs).
- To examine variant-specific expression (VSE) and the impact of inflammatory stimuli on DEFB4 expression.
Main Methods:
- DEFB4 expression was analyzed in LCLs and NHEKs.
- Cells were stimulated with lipopolysaccharide, tumor necrosis factor-alpha (TNF-alpha), and interferon-gamma (IFN-gamma).
- DEFB4 MSV was quantified in DNA and mRNA to assess VSE. The DEFB4 promoter region was resequenced.
Main Results:
- A strong correlation was observed between DEFB CN and DEFB4 expression in LCLs, though some cell lines with differing CNs showed similar expression.
- Quantification of DEFB4 MSV revealed VSE, with one variant consistently showing lower expression.
- Costimulation of NHEKs with TNF-alpha/IFN-gamma synergistically increased total DEFB4 expression and suppressed VSE.
- The DEFB4 promoter region exhibited a high density of sequence variations (approximately 1 MSV/41 bp).
Conclusions:
- DEFB copy number and sequence variations play a crucial role in regulating DEFB4 expression.
- Inflammatory signals can modulate DEFB4 expression and overcome variant-specific expression patterns.
- The high variability in the DEFB4 promoter suggests complex regulatory mechanisms influencing gene expression.
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