Small ribonucleic acids (smRNA) have been identified as important post-transcriptional regulators of gene expression. One important class of smRNA implicated in stress responses are natural antisense short interfering RNA (natsiRNA). These natsiRNAs are generated from two overlapping mRNA that are processed into short-interfering RNAs and target complementary mRNA sequences for degradation. A feature of natsiRNA is the inverse regulation of gene expression that is observed after environmental or developmental stimuli. Genome-wide expression analysis of hypoxia treated Arabidopsis roots in combination with the examination of gene expression in plants defective in natsiRNA processing, was used to find putative natsiRNA regulated genes. The results indicate the potential involvement of natsiRNA in regulating lipid signaling in hypoxia.