Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray.
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.
He
Housheng
H
Bioinformatics Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
Cai
Lun
L
Skogerbø
Geir
G
Deng
Wei
W
Liu
Tao
T
Zhu
Xiaopeng
X
Wang
Yudong
Y
Jia
Dong
D
Zhang
Zhihua
Z
Tao
Yong
Y
Zeng
Haipan
H
Aftab
Muhammad Nauman
MN
Cui
Yan
Y
Liu
Guozhen
G
Chen
Runsheng
R
D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D015870:Gene Expression; D020869:Gene Expression Profiling / Q000379:methods; D007438:Introns; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D012333:RNA, Messenger / Q000378:metabolism; D012342:RNA, Small Nuclear / Q000737:chemistry / Q000378:metabolism; D020537:RNA, Small Nucleolar / Q000737:chemistry / Q000378:metabolism; D022661:RNA, Untranslated / Q000235:genetics / Q000378:metabolism*
D012333:RNA, Messenger; D012342:RNA, Small Nuclear; D020537:RNA, Small Nucleolar; D022661:RNA, Untranslated