State Key Laboratory of Plant Genomics & National Plant Gene Research Centre (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China.
Mol Biotechnol. 2012 May;51(1):37-43. doi: 10.1007/s12033-011-9438-y.
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.
天然反义转录本（NATs）是含有与其他 RNA（通常称为有义转录本）反向互补序列的内源性转录本。NATs 在多种物种中调节有义转录本的表达。鉴定和分析 NATs 是阐明其功能的前提。微阵列是一种用于检测基因表达的全基因组方法。然而，传统的微阵列不包含 NATs 的特定探针；因此，它们不能用于检测 NATs。在本文中，我们开发了一种利用常规微阵列鉴定潜在 NATs 的新方法。在我们研究的这种方法中，我们用 Cy5 标记一个样本的第一链 cDNA，用 Cy3 标记另一个样本的第二链 cDNA，然后将这些标记的样本与寡核苷酸微阵列杂交。使用这种方法，我们在水稻品种 Nipponbare 中鉴定出了 920 个潜在的 NATs。在这些潜在的 NATs 中，有 88 个通过全长 cDNA 或定向 EST（表达序列标签）得到了证实。这是首次在水稻中使用常规寡核苷酸微阵列来鉴定 NATs。
