Novel endogenous antisense transcripts (data for the mouse normal tissues)

Recent transcriptomic analyses have uncovered widespread occurrence of natural antisense transcripts (NATs), which are transcribed from the opposite strand of another discrete transcribed region. We describe a novel probe-design technique for DNA microarray analysis that specifically targets the complementary strand of annotated genes, and show that this technique can successfully identify novel NAT expression in normal and tumor samples. Northern and in situ hybridization analyses of selected examples (Acaa1, Aard, and Thbd) confirmed their transcription and dynamic expression in a tissue- and cell-type-specific manner. Our data highlight the importance of NAT expression in the regulation of cellular processes and in oncogenesis. The fundamental basis of the technology described in this paper is applicable to all genes and sample types for the identification of NAT expression that is not possible by conventional cDNA/EST/CAGE information. Total RNA for the mouse (C57BL/6J) microarray experiments was isolated from SL10 cells (fibroblast cell line), brain, heart, intestine, kidney, liver, lung, placenta (d.p.c. 10.5 and 13.5), spleen, stomach, testis, and thymus. Testis was from C57BL/6J males (8 to 10 weeks), placenta was from pregnant mice, and the other tissue was from both male and female mice. Unpublished data has been masked in the supplementary feature extraction files.