Analysis of the p53/CEP-1 regulated non-coding transcriptome in C. elegans by an NSR-seq strategy.
In recent years, large numbers of non-coding RNAs (ncRNAs) have been identified in C. elegans but their functions are still not well studied. In C. elegans, CEP-1 is the sole homolog of the p53 family of genes. In order to obtain transcription profiles of ncRNAs regulated by CEP-1 under normal and UV stressed conditions, we applied the 'not-so-random' hexamers priming strategy to RNA sequencing in C. elegans, This NSR-seq strategy efficiently depleted rRNA transcripts from the samples and showed high technical replicability. We identified more than 1,000 ncRNAs whose apparent expression was repressed by CEP-1, while around 200 were activated. Around 40% of the CEP-1 activated ncRNAs promoters contain a putative CEP-1-binding site. CEP-1 regulated ncRNAs were frequently clustered and concentrated on the X chromosome. These results indicate that numerous ncRNAs are involved in CEP-1 transcriptional network and that these are especially enriched on the X chromosome in C. elegans.
Laboratory of Non-coding RNA, Institute of Biophysics, University of Chinese Academy of Sciences, Beijing, 100101, China.
Derong
D
Xu
Guifeng
G
Wei
Ping
P
Lu
Jianjun
J
Luo
Xiaomin
X
Chen
Geir
G
Skogerbø
Runsheng
R
Chen
D000818:Animals; D001665:Binding Sites; D017173:Caenorhabditis elegans; D029742:Caenorhabditis elegans Proteins / Q000235:genetics / Q000378:metabolism*; D059014:High-Throughput Nucleotide Sequencing; D011401:Promoter Regions, Genetic; D022661:RNA, Untranslated / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000528:radiation effects; D016159:Tumor Suppressor Protein p53 / Q000235:genetics / Q000378:metabolism*; D014466:Ultraviolet Rays; D014960:X Chromosome
C438244:CEP-1 protein, C elegans; D029742:Caenorhabditis elegans Proteins; D022661:RNA, Untranslated; D016159:Tumor Suppressor Protein p53