RT Journal
A1 Deng, Wei
A1 Zhu, Xiaopeng
A1 Skogerbø, Geir
A1 Zhao, Yi
A1 Fu, Zhuo
A1 Wang, Yudong
A1 He, Housheng
A1 Cai, Lun
A1 Sun, Hong
A1 Liu, Changning
A1 Li, Biao
A1 Bai, Baoyan
A1 Wang, Jie
A1 Jia, Dong
A1 Sun, Shiwei
A1 He, Hang
A1 Cui, Yan
A1 Wang, Yu
A1 Bu, Dongbo
A1 Chen, Runsheng
T1 Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression
JF Genome Research 
JO Genome Research 
YR 2006 
FD January 01 
VO 16 
IS 1 
SP 20 
OP 29 
DO 10.1101/gr.4139206 
UL http://genome.cshlp.org/content/16/1/20.abstract 
AB Recent evidence points to considerable transcription occurring in non-protein-coding regions of eukaryote genomes. However, their lack of conservation and demonstrated function have created controversy over whether these transcripts are functional. Applying a novel cloning strategy, we have cloned 100 novel and 61 known or predicted Caenorhabditis elegans full-length ncRNAs. Studying the genomic environment and transcriptional characteristics have shown that two-thirds of all ncRNAs, including many intronic snoRNAs, are independently transcribed under the control of ncRNA-specific upstream promoter elements. Furthermore, the transcription levels of at least 60% of the ncRNAs vary with developmental stages. We identified two new classes of ncRNAs, stem-bulge RNAs (sbRNAs) and snRNA-like RNAs (snlRNAs), both featuring distinct internal motifs, secondary structures, upstream elements, and high and developmentally variable expression. Most of the novel ncRNAs are conserved in Caenorhabditis briggsae, but only one homolog was found outside the nematodes. Preliminary estimates indicate that the C. elegans transcriptome contains ∼2700 small non-coding RNAs, potentially acting as regulatory elements in nematode development.