Analysis of differential gene expression profiles in Caenorhabditis elegans knockouts for the v‐SNARE master protein 1

Abstract

At chemical synapses, neurons communicate information to other cells by secreting neurotransmitters or neuropeptides into the synaptic cleft, which then bind to receptors on the target cell. Preliminary work performed in our laboratory has shown that mutant nematodes lacking a protein called VSM-1 have increased synaptic density compared with the wild type. Consequently, we hypothesized that genes expressed in vsm-1 mutants mediate enhanced synaptogenesis. To identify these genes of interest, we utilized microarray technology and quantitative PCR. To this end, first we isolated the total RNA from young-adult wild-type and vsm-1 mutant Caenorhabditis elegans. Next, we synthesized cDNA from reverse transcription of the isolated RNA. Hybridization of the cDNA to a microarray was performed to facilitate gene expression profiling. Finally, fluorescently labeled microarrays were analyzed, and the identities of induced and repressed genes were uncovered in the open-source software Magic Tool. Analyses of microarray experiments performed using three independent biological samples per strain and three technical replicas and dye swaps showed induction of genes coding for major sperm proteins and repression of SPP-2 in vsm-1 mutants. Microarray results were also validated and quantified by using quantitative PCR.