Analysis of gene function often involves detailed studies of when a given gene is expressed or silenced. Transposon mutagenesis is a powerful tool to generate insertional mutations that provide with a selectable marker and a reporter gene that can be used to analyze the transcriptional activity of a specific locus in a variety of microorganisms to study gene regulation. Then the reporter gene expression can be easily measured under different conditions to gain insight into the regulation of the particular locus of interest. We have used transposon mutagenesis as a tool to generate insertional mutations with a modified Tn7 transposon containing the reporter gene URA3 (Tn7-URA3) to study subtelomeric silencing in the opportunistic fungal pathogen Candida glabrata. This method consists of two major steps: an in vitro Tn7-URA3 mutagenesis of a plasmid containing the desired subtelomeric region to be analyzed, followed by homologous recombination into the target region of the C. glabrata genome. As an alternative, a fusion PCR protocol can also be used in which the URA3 reporter gene can be "fused" together with the 5' and 3' regions of the desired insertion point by a two step PCR protocol. This fusion product can be introduced into the C. glabrata genome by homologous recombination after transformation in the same way as the Tn7-URA3 mutagenesis products. Once the URA3 reporter gene has been introduced in the desired locus in the C. glabrata genome, a simple plate growth assay is performed to assess the expression of the reporter gene.