He Housheng, Cai Lun, Skogerbø Geir, Deng Wei, Liu Tao, Zhu Xiaopeng, Wang Yudong, Jia Dong, Zhang Zhihua, Tao Yong, Zeng Haipan, Aftab Muhammad Nauman, Cui Yan, Liu Guozhen, Chen Runsheng
Bioinformatics Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
Nucleic Acids Res. 2006 May 31;34(10):2976-83. doi: 10.1093/nar/gkl371. Print 2006.
Small non-coding RNAs (ncRNAs) are encoded by genes that function at the RNA level, and several hundred ncRNAs have been identified in various organisms. Here we describe an analysis of the small non-coding transcriptome of Caenorhabditis elegans, microRNAs excepted. As a substantial fraction of the ncRNAs is located in introns of protein-coding genes in C.elegans, we also analysed the relationship between ncRNA and host gene expression. To this end, we designed a combined microarray, which included probes against ncRNA as well as host gene mRNA transcripts. The microarray revealed pronounced differences in expression profiles, even among ncRNAs with housekeeping functions (e.g. snRNAs and snoRNAs), indicating distinct developmental regulation and stage-specific functions of a number of novel transcripts. Analysis of ncRNA-host mRNA relations showed that the expression of intronic ncRNA loci with conserved upstream motifs was not correlated to (and much higher than) expression levels of their host genes. Even promoter-less intronic ncRNA loci, though showing a clear correlation to host gene expression, appeared to have a surprising amount of 'expressional freedom', depending on host gene function. Taken together, our microarray analysis presents a more complete and detailed picture of a non-coding transcriptome than hitherto has been presented for any other multicellular organism.
小非编码RNA（ncRNAs）由在RNA水平发挥作用的基因编码，并且在各种生物体中已鉴定出数百种ncRNAs。本文我们描述了对秀丽隐杆线虫小非编码转录组（不包括微小RNA）的分析。由于秀丽隐杆线虫中相当一部分ncRNAs位于蛋白质编码基因的内含子中，我们还分析了ncRNA与宿主基因表达之间的关系。为此，我们设计了一种组合微阵列，其中包括针对ncRNA以及宿主基因mRNA转录本的探针。该微阵列揭示了表达谱中的显著差异，即使在具有管家功能的ncRNAs（如小核RNA和核仁小RNA）之间也是如此，这表明许多新转录本具有独特的发育调控和阶段特异性功能。对ncRNA与宿主mRNA关系的分析表明，具有保守上游基序的内含子ncRNA基因座的表达与其宿主基因的表达水平不相关（且远高于宿主基因表达水平）。即使是无启动子的内含子ncRNA基因座，尽管与宿主基因表达有明显相关性，但似乎也具有惊人数量的“表达自由度”，这取决于宿主基因的功能。综上所述，我们的微阵列分析呈现了一幅比迄今为止任何其他多细胞生物更完整、更详细的非编码转录组图景。
