Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray.
Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray.
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使用组合微阵列分析秀丽隐杆线虫非编码 RNA 表达
DOI：
10.1093/nar/gkl371
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发表时间：
2006
影响因子：
14.9
通讯作者：
Chen R
中科院分区：
文献类型：
--
作者：
He H;Cai L;Skogerbø G;Deng W;Liu T;Zhu X;Wang Y;Jia D;Zhang Z;Tao Y;Zeng H;Aftab MN;Cui Y;Liu G;Chen R
小的非编码RNA（ncRNA）由在RNA水平上起作用的基因编码，并且已经在各种生物体中鉴定了数百种ncRNA。在这里，我们描述了一个小的非编码的秀丽隐杆线虫的转录组的分析，microRNA除外。由于大部分ncRNA位于线虫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，我们设计了一个组合的微阵列，其中包括针对ncRNA以及宿主基因mRNA转录物的探针。微阵列揭示了表达谱的显著差异，甚至在具有管家功能的ncRNA（例如snRNA和snoRNA）之间，表明许多新转录物的不同发育调节和阶段特异性功能。ncRNA-宿主mRNA关系的分析表明，具有保守上游基序的内含子ncRNA位点的表达与其宿主基因的表达水平不相关（并且远高于）。即使启动子的内含子ncRNA位点，虽然显示出明显的相关性，宿主基因表达，似乎有一个令人惊讶的量的“表达自由”，这取决于宿主基因的功能。总而言之，我们的微阵列分析提供了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片。
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.
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DOI：
10.1073/pnas.79.4.1195
发表时间：
1982-01-01
期刊：
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA-BIOLOGICAL SCIENCES
影响因子：
--
作者：
CILIBERTO, G;CASTAGNOLI, L;CORTESE, R
通讯作者：
CORTESE, R
DOI：
10.1073/pnas.1533509100
发表时间：
2003-08-05
影响因子：
11.1
作者：
Dominski, Z;Yang, XC;Marzluff, WF
通讯作者：
Marzluff, WF
影响因子：
56.9
作者：
Thompson, M;Haeusler, RA;Engelke, DR
通讯作者：
Engelke, DR
影响因子：
10.5
作者：
Rinn, JL;Euskirchen, G;Snyder, M
通讯作者：
Snyder, M
影响因子：
5.3
作者：
Evans, D;Blumenthal, T
通讯作者：
Blumenthal, T