Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray

doi:10.1093/nar/gkl371

	Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray
	He, Housheng ; Cai, Lun ; Skogerbo, 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
	2006
发表期刊	NUCLEIC ACIDS RESEARCH
ISSN	0305-1048
卷号	34 期号:10 页码:2976-2983
摘要	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.
DOI	10.1093/nar/gkl371
收录类别	SCI
语种	英语
WOS研究方向	Biochemistry & Molecular Biology
WOS类目	Biochemistry & Molecular Biology
WOS记录号	WOS:000239430900013
出版者	OXFORD UNIV PRESS
引用统计	被引频次：27[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/2XEOYT63/10502
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Chen, Runsheng
作者单位	1.Chinese Acad Sci, Inst Biophys, Bioinformat Lab, Beijing 100101, Peoples R China 2.Chinese Acad Sci, Natl Lab Biomacromol, Inst Biophys, Beijing 100101, Peoples R China 3.Chinese Acad Sci, Inst Comp Technol, Computat Biol Res Grp, Div Intelligent Software Syst, Beijing 100080, Peoples R China 4.Chinese Natl Human Genome Ctr, Beijing 100176, Peoples R China 5.Univ Tennessee, Hlth Sci Ctr, Dept Mol Sci, Ctr Gen & Bioinformat, Memphis, TN 38163 USA 6.Chinese Acad Sci, Grad Sch, Beijing 100080, Peoples R China 7.Chinese Acad Sci, Beijing Gen Inst, Beijing 101300, Peoples R China 8.Chinese Acad Sci, Inst Genet & Dev Biol, Beijing, Peoples R China
推荐引用方式 GB/T 7714	He, Housheng,Cai, Lun,Skogerbo, Geir,et al. Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray[J]. NUCLEIC ACIDS RESEARCH,2006,34(10):2976-2983.
APA	He, Housheng.,Cai, Lun.,Skogerbo, Geir.,Deng, Wei.,Liu, Tao.,...&Chen, Runsheng.(2006).Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray.NUCLEIC ACIDS RESEARCH,34(10),2976-2983.
MLA	He, Housheng,et al."Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray".NUCLEIC ACIDS RESEARCH 34.10(2006):2976-2983.