1.Analysis of the p53/CEP-1 regulated non-coding transcriptome in C. elegans by an NSR-seq strategy.
Derong XU ; Guifeng WEI ; Ping LU ; Jianjun LUO ; Xiaomin CHEN ; Geir SKOGERBØ ; Runsheng CHEN
Protein & Cell 2014;5(10):770-782
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.
Animals
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Binding Sites
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Caenorhabditis elegans
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Caenorhabditis elegans Proteins
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genetics
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metabolism
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High-Throughput Nucleotide Sequencing
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Promoter Regions, Genetic
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RNA, Untranslated
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metabolism
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Sequence Analysis, RNA
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Transcriptome
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radiation effects
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Tumor Suppressor Protein p53
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genetics
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metabolism
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Ultraviolet Rays
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X Chromosome