title: Both copy number and sequence variations affect expression of human DEFB4.
abstract: Copy number variations (CNVs) were found to contribute massively to the variability of genomes. One of the best studied CNV region is the beta-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 beta-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-alpha (TNF-alpha) and interferon-gamma (IFN-gamma). Moreover, we quantified one DEFB4 MSV in DNA and mRNA as a marker for variant-specific expression (VSE) and resequenced a region of approximately 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-alpha/IFN-gamma 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 (approximately 1 MSV/41 bp).
authors.affiliation: Genome Analysis, Leibniz Institute for Age Research-Fritz Lipmann Institute, Jena, Germany. mgroth@fli-leibniz.de
authors.forename: M
authors.initials: M
authors.lastname: Groth
authors.forename: C
authors.initials: C
authors.lastname: Wiegand
authors.forename: K
authors.initials: K
authors.lastname: Szafranski
authors.forename: K
authors.initials: K
authors.lastname: Huse
authors.forename: M
authors.initials: M
authors.lastname: Kramer
authors.forename: P
authors.initials: P
authors.lastname: Rosenstiel
authors.forename: S
authors.initials: S
authors.lastname: Schreiber
authors.forename: J
authors.initials: J
authors.lastname: Norgauer
authors.forename: M
authors.initials: M
authors.lastname: Platzer
mesh_terms: D001483:Base Sequence; D002478:Cells, Cultured; D056915:DNA Copy Number Variations / Q000235:genetics*; D005786:Gene Expression Regulation; D014644:Genetic Variation / Q000235:genetics; D006239:Haplotypes / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic / Q000235:genetics; D023083:beta-Defensins / Q000096:biosynthesis* / Q000235:genetics*
chemical_list: C106641:DEFB4A protein, human; D023083:beta-Defensins