The Caenorhabditis elegans intermediate-size transcriptome shows high degree of stage-specific expression
Earlier studies have revealed a substantial amount of transcriptional activity occurring outside annotated protein-coding genes of the Caenorhabditis elegans genome. One important fraction of this transcriptional activity relates to intermediate-size (70–500 nt) transcripts (is-ncRNAs) of mostly unk...
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| Format: | Online |
| Language: | English |
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Oxford University Press
2011
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3130273/ |
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pubmed-31302732011-07-06 The Caenorhabditis elegans intermediate-size transcriptome shows high degree of stage-specific expression Wang, Yunfei Chen, Jingjing Wei, Guifeng He, Housheng Zhu, Xiaopeng Xiao, Tengfei Yuan, Jiao Dong, Bo He, Shunmin Skogerbø, Geir Chen, Runsheng RNA Earlier studies have revealed a substantial amount of transcriptional activity occurring outside annotated protein-coding genes of the Caenorhabditis elegans genome. One important fraction of this transcriptional activity relates to intermediate-size (70–500 nt) transcripts (is-ncRNAs) of mostly unknown function. Profiling the expression of this segment of the transcriptome on a tiling array through the C. elegans life cycle identified 5866 hitherto unannotated transcripts. The novel loci were distributed across intronic and intergenic space, with some enrichment toward protein-coding gene termini. The majority of the putative is-ncRNAs showed either stage-specific expression, or distinct developmental variation in their expression levels. More than 200 loci showed male-specific expression, and conserved loci were significantly enriched on the X chromosome, both observations strongly suggesting involvement of is-ncRNAs in sex-specific functions. Half of the novel loci were conserved in other nematodes, and numerous loci showed significant conservational correlations to nearby coding genes. Assuming functional roles for most of the novel loci, the data imply a nematode is-ncRNA tool kit of considerable size and variety. Oxford University Press 2011-07 2011-03-04 /pmc/articles/PMC3130273/ /pubmed/21378118 http://dx.doi.org/10.1093/nar/gkr102 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
| 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 |
Wang, Yunfei Chen, Jingjing Wei, Guifeng He, Housheng Zhu, Xiaopeng Xiao, Tengfei Yuan, Jiao Dong, Bo He, Shunmin Skogerbø, Geir Chen, Runsheng |
| spellingShingle |
Wang, Yunfei Chen, Jingjing Wei, Guifeng He, Housheng Zhu, Xiaopeng Xiao, Tengfei Yuan, Jiao Dong, Bo He, Shunmin Skogerbø, Geir Chen, Runsheng The Caenorhabditis elegans intermediate-size transcriptome shows high degree of stage-specific expression |
| author_facet |
Wang, Yunfei Chen, Jingjing Wei, Guifeng He, Housheng Zhu, Xiaopeng Xiao, Tengfei Yuan, Jiao Dong, Bo He, Shunmin Skogerbø, Geir Chen, Runsheng |
| author_sort |
Wang, Yunfei |
| title |
The Caenorhabditis elegans intermediate-size transcriptome shows high degree of stage-specific expression |
| title_short |
The Caenorhabditis elegans intermediate-size transcriptome shows high degree of stage-specific expression |
| title_full |
The Caenorhabditis elegans intermediate-size transcriptome shows high degree of stage-specific expression |
| title_fullStr |
The Caenorhabditis elegans intermediate-size transcriptome shows high degree of stage-specific expression |
| title_full_unstemmed |
The Caenorhabditis elegans intermediate-size transcriptome shows high degree of stage-specific expression |
| title_sort |
caenorhabditis elegans intermediate-size transcriptome shows high degree of stage-specific expression |
| description |
Earlier studies have revealed a substantial amount of transcriptional activity occurring outside annotated protein-coding genes of the Caenorhabditis elegans genome. One important fraction of this transcriptional activity relates to intermediate-size (70–500 nt) transcripts (is-ncRNAs) of mostly unknown function. Profiling the expression of this segment of the transcriptome on a tiling array through the C. elegans life cycle identified 5866 hitherto unannotated transcripts. The novel loci were distributed across intronic and intergenic space, with some enrichment toward protein-coding gene termini. The majority of the putative is-ncRNAs showed either stage-specific expression, or distinct developmental variation in their expression levels. More than 200 loci showed male-specific expression, and conserved loci were significantly enriched on the X chromosome, both observations strongly suggesting involvement of is-ncRNAs in sex-specific functions. Half of the novel loci were conserved in other nematodes, and numerous loci showed significant conservational correlations to nearby coding genes. Assuming functional roles for most of the novel loci, the data imply a nematode is-ncRNA tool kit of considerable size and variety. |
| publisher |
Oxford University Press |
| publishDate |
2011 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3130273/ |
| _version_ |
1611463888873717760 |