Microarray analysis of ncRNA expression patterns in Caenorhabditis elegans after RNAi against snoRNA associated proteins.
Microarray analysis of ncRNA expression patterns in Caenorhabditis elegans after RNAi against snoRNA associated proteins.
复制标题
针对 snoRNA 相关蛋白进行 RNAi 后，对秀丽隐杆线虫中 ncRNA 表达模式进行微阵列分析
DOI：
10.1186/1471-2164-9-278
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发表时间：
2008-06-11
期刊：
影响因子：
4.4
通讯作者：
Chen, Runsheng
中科院分区：
文献类型：
--
作者：
Aftab, Muhammad Nauman;He, Housheng;Skogerbo, Geir;Chen, Runsheng
背景
短的非编码RNA（ncRNA）在核糖核蛋白（RNP）复合物中执行其细胞功能，这对于维持ncRNA的稳定性也是必不可少的。因此，通过RNA干扰（RNAi）消耗非编码核糖核蛋白（ncRNP）颗粒的单个蛋白组分可能会影响相应ncRNA的表达水平，并且在研究ncRNA-蛋白质相互作用和ncRNA功能时，消耗候选相关蛋白可能构成替代策略。因此，我们进行了一项初步研究，在ncRNA微阵列上观察RNAi对秀丽隐杆线虫小核仁RNP（snoRNP）蛋白组分的影响。
结果
针对单个C. snoRNP的elegans蛋白组分产生了强烈降低的mRNA水平和所有靶蛋白的不同表型。对于每种类型的snoRNP，单独去除四种蛋白质组分中的至少三种，相应的小核仁RNA（snoRNA）的表达水平显著降低（P <1.2 × 10-5），而其他ncRNA的表达水平基本不受影响。个别蛋白质的消耗的影响是根据snoRNP结构分析，在其他物种中获得的所有，但两个八个目标蛋白。snoRNA的大小，序列和二级结构特征的变化没有系统地反映在单个蛋白质组分的snoRNP的亲和力。这些数据支持几乎所有注释的snoRNA的分类，并表明在未分类的短ncRNA转录本中存在几种新的snoRNA。一些含有典型Sm结合元件序列（Sm Y RNA）的转录本也显示出C/D盒snoRNP的蛋白组分耗尽后表达减少，而一些茎凸起RNA（sbRNA）的表达增加耗尽相同的蛋白质后。
结论
该研究证实了对其他生物体的观察结果，其中注意到ncRNP的蛋白质组分耗尽后ncRNA水平降低，并表明这种表达水平的降低发生在整个ncRNA组中。因此，该研究还证明了将针对候选蛋白质的RNAi与ncRNA微阵列分析相结合以研究ncRNA-蛋白质相互作用并因此研究ncRNA细胞功能的可行性。
Background
Short non-coding RNAs (ncRNAs) perform their cellular functions in ribonucleoprotein (RNP) complexes, which are also essential for maintaining the stability of the ncRNAs. Depletion of individual protein components of non-coding ribonucleoprotein (ncRNP) particles by RNA interference (RNAi) may therefore affect expression levels of the corresponding ncRNA, and depletion of candidate associated proteins may constitute an alternative strategy when investigating ncRNA-protein interactions and ncRNA functions. Therefore, we carried out a pilot study in which the effects of RNAi against protein components of small nucleolar RNPs (snoRNPs) in Caenorhabditis elegans were observed on an ncRNA microarray.
Results
RNAi against individual C. elegans protein components of snoRNPs produced strongly reduced mRNA levels and distinct phenotypes for all targeted proteins. For each type of snoRNP, individual depletion of at least three of the four protein components produced significant (P ≦ 1.2 × 10-5) reductions in the expression levels of the corresponding small nucleolar RNAs (snoRNAs), whereas the expression levels of other ncRNAs were largely unaffected. The effects of depletion of individual proteins were in accordance with snoRNP structure analyses obtained in other species for all but two of the eight targeted proteins. Variations in snoRNA size, sequence and secondary structure characteristics were not systematically reflected in the affinity for individual protein component of snoRNPs. The data supported the classification of nearly all annotated snoRNAs and suggested the presence of several novel snoRNAs among unclassified short ncRNA transcripts. A number of transcripts containing canonical Sm binding element sequences (Sm Y RNAs) also showed reduced expression after depletion of protein components of C/D box snoRNPs, whereas the expression of some stem-bulge RNAs (sbRNAs) was increased after depletion of the same proteins.
Conclusion
The study confirms observations made for other organisms, where reduced ncRNA levels after depletion of protein components of ncRNPs were noted, and shows that such reductions in expression levels occur across entire sets of ncRNA. Thereby, the study also demonstrates the feasibility of combining RNAi against candidate proteins with ncRNA microarray analysis to investigate ncRNA-protein interactions and hence ncRNA cellular functions.
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影响因子：
56.9
作者：
Cheng, J;Kapranov, P;Gingeras, TR
通讯作者：
Gingeras, TR
使用组合微阵列分析秀丽隐杆线虫非编码 RNA 表达
影响因子：
14.9
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
通讯作者：
Chen R
DOI：
10.1073/pnas.141004698
发表时间：
2001-07-17
影响因子：
11.1
作者：
Hanazawa, M;Mochii, M;Iino, Y
通讯作者：
Iino, Y
影响因子：
10.5
作者：
Ganot, P;CaizerguesFerrer, M;Kiss, T
通讯作者：
Kiss, T
影响因子：
10.5
作者：
Hogg, J. Robert;Collins, Kathleen
通讯作者：
Collins, Kathleen