Generalized atrophic benign epidermolysis bullosa [GABEB (OMIM no. 226650)] is an inherited subepidermal blistering disease typically caused by null mutations in COL17A1, the gene encoding type XVII collagen. Studies of GABEB keratinocytes homozygous for 4003delTC showed that this 2 bp deletion results in markedly reduced COL17A1 transcripts due to nonsense mediated-mRNA decay. To explore consequences of this null mutation in COL17A1 on the expression of other genes, RNA samples from reference GABEB and normal keratinocytes were profiled in comparative screens of microarrays of known cDNAs (n = 6180) and expressed sequence tags (ESTs) (n = 15 144). All comparative hybridization experiments were performed > or = twice; data were quantitated by densitometry and analyzed using peak quantification statistical comparative analysis (P-SCAN) software to identify differentially expressed genes. Representative genes found to be differentially expressed were verified using real-time reverse transcription-polymerase chain reaction (RT-PCR). These experiments determined that expression of nonsense-mediated mRNA decay trans-acting factor (NMD-F), the regulator of nonsense transcripts (i.e. the human homolog of the yeast Upf1 protein), was upregulated in GABEB keratinocytes. NMD-F was subsequently found to be upregulated in cultured keratinocytes from other GABEB patients homozygous for 4003delTC. These findings indicate that the gene responsible for nonsense-mediated mRNA decay is upregulated in keratinocytes known to eliminate mutant COL17A1 transcripts via this highly conserved mechanism.