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Detection of intergenic non-coding RNAs expressed in the main developmental stages in Drosophila melanogaster
How many intergenically encoded non-coding RNAs (ncRNAs) are expressed during various developmental stages in Drosophila? Previous analyses in one or a few developmental stages indicated abundant expression of intergenic ncRNAs. However, some reported that ncRNAs have been recently falsified, and, i...
Autores principales: | , , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2009
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715228/ https://www.ncbi.nlm.nih.gov/pubmed/19451167 http://dx.doi.org/10.1093/nar/gkp334 |
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author | Li, Zheng Liu, Min Zhang, Li Zhang, Wenxia Gao, Ge Zhu, Zuoyan Wei, Liping Fan, Qichang Long, Manyuan |
author_facet | Li, Zheng Liu, Min Zhang, Li Zhang, Wenxia Gao, Ge Zhu, Zuoyan Wei, Liping Fan, Qichang Long, Manyuan |
author_sort | Li, Zheng |
collection | PubMed |
description | How many intergenically encoded non-coding RNAs (ncRNAs) are expressed during various developmental stages in Drosophila? Previous analyses in one or a few developmental stages indicated abundant expression of intergenic ncRNAs. However, some reported that ncRNAs have been recently falsified, and, in general, the false positive rate for ncRNA detection is unknown. In this report, we used reverse transcription-PCR (RT-PCR), a more robust method, to detect ncRNAs from the intergenic regions that are expressed in four major developmental stages (6–8 h embryo, 20–22 h embryo, larvae and adult). We tested 1027 regions, ∼10% of all intergenic regions, and detected transcription by RT–PCR. The results from 18 342 RT–PCR experiments revealed evidence for transcription in 72.7% of intergenic regions in the developmental process. The early developmental stage appears to be associated with more abundant ncRNAs than later developmental stages. In the early stage, we detected 43.6% of intergenic regions that encode transcripts in the triplicate RT–PCR experiments, yielding an estimate of 5006 intergenic regions in the entire genome likely encoding ncRNAs. We compared the RT–PCR-related approach with previous tiling array-based approach and observed that the latter method is insensitive to short ncRNAs, especially the molecules less than 120 bp. We measured false positive rates for the analyzed genomic approaches including the RT–PCR and tiling array method. |
format | Text |
id | pubmed-2715228 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-27152282009-07-24 Detection of intergenic non-coding RNAs expressed in the main developmental stages in Drosophila melanogaster Li, Zheng Liu, Min Zhang, Li Zhang, Wenxia Gao, Ge Zhu, Zuoyan Wei, Liping Fan, Qichang Long, Manyuan Nucleic Acids Res Genomics How many intergenically encoded non-coding RNAs (ncRNAs) are expressed during various developmental stages in Drosophila? Previous analyses in one or a few developmental stages indicated abundant expression of intergenic ncRNAs. However, some reported that ncRNAs have been recently falsified, and, in general, the false positive rate for ncRNA detection is unknown. In this report, we used reverse transcription-PCR (RT-PCR), a more robust method, to detect ncRNAs from the intergenic regions that are expressed in four major developmental stages (6–8 h embryo, 20–22 h embryo, larvae and adult). We tested 1027 regions, ∼10% of all intergenic regions, and detected transcription by RT–PCR. The results from 18 342 RT–PCR experiments revealed evidence for transcription in 72.7% of intergenic regions in the developmental process. The early developmental stage appears to be associated with more abundant ncRNAs than later developmental stages. In the early stage, we detected 43.6% of intergenic regions that encode transcripts in the triplicate RT–PCR experiments, yielding an estimate of 5006 intergenic regions in the entire genome likely encoding ncRNAs. We compared the RT–PCR-related approach with previous tiling array-based approach and observed that the latter method is insensitive to short ncRNAs, especially the molecules less than 120 bp. We measured false positive rates for the analyzed genomic approaches including the RT–PCR and tiling array method. Oxford University Press 2009-07 2009-05-18 /pmc/articles/PMC2715228/ /pubmed/19451167 http://dx.doi.org/10.1093/nar/gkp334 Text en © 2009 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Genomics Li, Zheng Liu, Min Zhang, Li Zhang, Wenxia Gao, Ge Zhu, Zuoyan Wei, Liping Fan, Qichang Long, Manyuan Detection of intergenic non-coding RNAs expressed in the main developmental stages in Drosophila melanogaster |
title | Detection of intergenic non-coding RNAs expressed in the main developmental stages in Drosophila melanogaster |
title_full | Detection of intergenic non-coding RNAs expressed in the main developmental stages in Drosophila melanogaster |
title_fullStr | Detection of intergenic non-coding RNAs expressed in the main developmental stages in Drosophila melanogaster |
title_full_unstemmed | Detection of intergenic non-coding RNAs expressed in the main developmental stages in Drosophila melanogaster |
title_short | Detection of intergenic non-coding RNAs expressed in the main developmental stages in Drosophila melanogaster |
title_sort | detection of intergenic non-coding rnas expressed in the main developmental stages in drosophila melanogaster |
topic | Genomics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715228/ https://www.ncbi.nlm.nih.gov/pubmed/19451167 http://dx.doi.org/10.1093/nar/gkp334 |
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