Analysis of the p53/CEP-1 regulated non-coding transcriptome in C. elegans by an NSR-seq strategy.
10.1007/s13238-014-0071-y
- Author:
Derong XU
1
;
Guifeng WEI
;
Ping LU
;
Jianjun LUO
;
Xiaomin CHEN
;
Geir SKOGERBØ
;
Runsheng CHEN
Author Information
1. Laboratory of Non-coding RNA, Institute of Biophysics, University of Chinese Academy of Sciences, Beijing, 100101, China.
- Publication Type:Journal Article
- MeSH:
Animals;
Binding Sites;
Caenorhabditis elegans;
Caenorhabditis elegans Proteins;
genetics;
metabolism;
High-Throughput Nucleotide Sequencing;
Promoter Regions, Genetic;
RNA, Untranslated;
metabolism;
Sequence Analysis, RNA;
Transcriptome;
radiation effects;
Tumor Suppressor Protein p53;
genetics;
metabolism;
Ultraviolet Rays;
X Chromosome
- From:
Protein & Cell
2014;5(10):770-782
- CountryChina
- Language:English
-
Abstract:
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.