Microarray analysis of ncRNA expression patterns in Caenorhabditis elegans after RNAi against snoRNA associated proteins

doi:10.1186/1471-2164-9-278

	Microarray analysis of ncRNA expression patterns in Caenorhabditis elegans after RNAi against snoRNA associated proteins
	Aftab, Muhammad Nauman 1,2,3; He, Housheng 1,2,3; Skogerbo, Geir 1,2; Chen, Runsheng 1,2,3,4
	2008-06-11
发表期刊	BMC GENOMICS
ISSN	1471-2164
卷号	9 页码:9
摘要	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 x 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.
DOI	10.1186/1471-2164-9-278
收录类别	SCI
语种	英语
WOS研究方向	Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS类目	Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS记录号	WOS:000257358900002
出版者	BIOMED CENTRAL LTD
引用统计	被引频次：14[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/11088
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Skogerbo, Geir
作者单位	1.Chinese Acad Sci, Inst Biophys, Bioinformat Lab, Beijing 100101, Peoples R China 2.Chinese Acad Sci, Inst Biophys, Natl Lab Biomacromol, Beijing 100101, Peoples R China 3.Chinese Acad Sci, Bioinformat Res Grp, Key Lab Intelligent Informat Proc, Inst Comp Technol,Grad Sch, Beijing 100080, Peoples R China 4.Chinese Natl Human Genome Ctr, Beijing 100176, Peoples R China
推荐引用方式 GB/T 7714	Aftab, Muhammad Nauman,He, Housheng,Skogerbo, Geir,et al. Microarray analysis of ncRNA expression patterns in Caenorhabditis elegans after RNAi against snoRNA associated proteins[J]. BMC GENOMICS,2008,9:9.
APA	Aftab, Muhammad Nauman,He, Housheng,Skogerbo, Geir,&Chen, Runsheng.(2008).Microarray analysis of ncRNA expression patterns in Caenorhabditis elegans after RNAi against snoRNA associated proteins.BMC GENOMICS,9,9.
MLA	Aftab, Muhammad Nauman,et al."Microarray analysis of ncRNA expression patterns in Caenorhabditis elegans after RNAi against snoRNA associated proteins".BMC GENOMICS 9(2008):9.