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 U...
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| Format: | Online |
| Language: | English |
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Higher Education Press
2014
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4180458/ |
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pubmed-41804582014-10-08 Analysis of the p53/CEP-1 regulated non-coding transcriptome in C. elegans by an NSR-seq strategy Xu, Derong Wei, Guifeng Lu, Ping Luo, Jianjun Chen, Xiaomin Skogerbø, Geir Chen, Runsheng Research Article 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. Higher Education Press 2014-05-21 2014-10 /pmc/articles/PMC4180458/ /pubmed/24844773 http://dx.doi.org/10.1007/s13238-014-0071-y Text en © The Author(s) 2014 Open AccessThis article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited. |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Xu, Derong Wei, Guifeng Lu, Ping Luo, Jianjun Chen, Xiaomin Skogerbø, Geir Chen, Runsheng |
| spellingShingle |
Xu, Derong Wei, Guifeng Lu, Ping Luo, Jianjun Chen, Xiaomin Skogerbø, Geir Chen, Runsheng Analysis of the p53/CEP-1 regulated non-coding transcriptome in C. elegans by an NSR-seq strategy |
| author_facet |
Xu, Derong Wei, Guifeng Lu, Ping Luo, Jianjun Chen, Xiaomin Skogerbø, Geir Chen, Runsheng |
| author_sort |
Xu, Derong |
| title |
Analysis of the p53/CEP-1 regulated
non-coding transcriptome in C. elegans by an NSR-seq
strategy |
| title_short |
Analysis of the p53/CEP-1 regulated
non-coding transcriptome in C. elegans by an NSR-seq
strategy |
| title_full |
Analysis of the p53/CEP-1 regulated
non-coding transcriptome in C. elegans by an NSR-seq
strategy |
| title_fullStr |
Analysis of the p53/CEP-1 regulated
non-coding transcriptome in C. elegans by an NSR-seq
strategy |
| title_full_unstemmed |
Analysis of the p53/CEP-1 regulated
non-coding transcriptome in C. elegans by an NSR-seq
strategy |
| title_sort |
analysis of the p53/cep-1 regulated
non-coding transcriptome in c. elegans by an nsr-seq
strategy |
| description |
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. |
| publisher |
Higher Education Press |
| publishDate |
2014 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4180458/ |
| _version_ |
1613139183959801856 |