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 Unpublished data has been masked in the supplementary feature extraction files.近年来的转录组学分析证实，天然反义转录本（natural antisense transcripts, NATs）广泛存在——此类转录本由另一独立转录区域的反向互补链转录产生。本研究报道一种用于DNA微阵列分析的新型探针设计技术，该技术可特异性靶向注释基因的互补链，并证实其能够成功在正常与肿瘤样本中鉴定出新型天然反义转录本的表达。针对选定靶标（Acaa1、Aard及Thbd）开展的Northern印迹杂交与原位杂交分析，验证了这些转录本的转录活性，以及其在组织与细胞类型特异性模式下的动态表达特征。本研究数据凸显了天然反义转录本表达在细胞进程调控及肿瘤发生发展中的重要作用。本文所述技术的核心原理可推广至所有基因与样本类型，用于鉴定通过传统互补DNA（complementary DNA, cDNA）/表达序列标签（expressed sequence tag, EST）/帽分析基因表达（cap analysis of gene expression, CAGE）信息无法发现的天然反义转录本表达。小鼠（C57BL/6J）微阵列实验所用总RNA提取自SL10细胞（成纤维细胞系）、脑、心脏、肠道、肾脏、肝脏、肺、胎盘（妊娠天数10.5与13.5）、脾脏、胃、睾丸及胸腺。睾丸样本取自8至10周龄的C57BL/6J雄性小鼠，胎盘样本取自妊娠小鼠，其余组织样本则同时取自雌雄小鼠。补充特征提取文件中已隐去未发表数据。