Identification of potential antisense transcripts in rice using conventional microarray

Natural antisense transcripts (NATs) are endogenous transcripts that contain reverse complementary sequences to other RNAs (usually called sense transcripts). NATs regulate the expression of sense transcripts in a wide range of species. The identification and analysis of NATs are the prerequisite to elucidate their functions. Microarray is a genome-wide method to detect gene expression. However, conventional microarrays do not contain the specific probes of NATs; thus, they cannot be utilized to detect NATs. In this article, we developed a novel method to identify potential NATs with the conventional microarrays. In this method of our study, we labeled the first strand cDNA from one sample with Cy5 and labeled the second strand cDNA from another sample with Cy3, and then hybridized these labeled samples with oligonucleotide microarray. Using this method, we identified 920 potential NATs in rice variety Nipponbare. Among these potential NATs, 88 of them were confirmed by either full-length cDNA or orientated ESTs (expressed sequence tags). This is the first time that a conventional oligonucleotide microarray was employed to identify NATs in rice.