RESEARCH ARTICLE

Analysis of the p53/CEP-1 regulated non-coding transcriptome in C. elegans by an NSR-seq strategy

  • Derong Xu 1,2 ,
  • Guifeng Wei 1,2 ,
  • Ping Lu 3 ,
  • Jianjun Luo 1 ,
  • Xiaomin Chen 1 ,
  • Geir Skogerbø 1 ,
  • Runsheng Chen , 1
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  • 1. Laboratory of Non-coding RNA, Institute of Biophysics, University of Chinese Academy of Sciences, Beijing 100101, China
  • 2. Graduate University of Chinese Academy of Sciences, Beijing 100080, China
  • 3. Key Laboratory of Forest Protection, State Forestry Administration/Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China

Received date: 17 Mar 2014

Accepted date: 09 Apr 2014

Published date: 24 Oct 2014

Copyright

2014 This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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-sorandom’ 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.

Cite this article

Derong Xu , Guifeng Wei , Ping Lu , Jianjun Luo , Xiaomin Chen , Geir Skogerbø , Runsheng Chen . Analysis of the p53/CEP-1 regulated non-coding transcriptome in C. elegans by an NSR-seq strategy[J]. Protein & Cell, 2014 , 5(10) : 770 -782 . DOI: 10.1007/s13238-014-0071-y

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