Detection of intergenic non-coding RNAs expressed in the main developmental stages in Drosophila melanogaster
نویسندگان
چکیده
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, approximately 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.
منابع مشابه
Comparative Expression Dynamics of Intergenic Long Noncoding RNAs in the Genus Drosophila
Thousands of long noncoding RNAs (lncRNAs) have been annotated in eukaryotic genomes, but comparative transcriptomic approaches are necessary to understand their biological impact and evolution. To facilitate such comparative studies in Drosophila, we identified and characterized lncRNAs in a second Drosophilid-the evolutionary model Drosophila pseudoobscura Using RNA-Seq and computational filt...
متن کاملDysregulated Expression of Long Intergenic Non-coding RNAs (LincRNAs) in Urothelial Bladder Carcinoma
Long intergenic non-coding RNA (lincRNA) has been introduced as key regulators of diverse biological processes, including transcription, chromatin organization, cell growth and tumorigenesis. With regard to the potential role of lincRNAs in cancer development, one may postulate that differential expression of lincRNAs could be employed as a tool in cancer diagnosis, prognosis, and targeted ther...
متن کاملAconitase and Developmental EndPointsasEarly IndicatorsofCellularToxicity Induced by Xenobiotics in Drosophila Melanogaster
Background: In this study, the toxicity of the different xenobiotics was tested on the fruit fly Drosophila melanogaster model system. Methods: Fly larvae were raised on food supplemented with xenobioticsat different concentrations (sodium nitroprusside (0.1-1.5 mM), S-nitrosoglutathione (0.5-4 mM), and potassium ferrocyanide (1 mM)). Emergence of flies, food intake by larvae, and pupation h...
متن کاملRNomics in Drosophila melanogaster: identi®cation of 66 candidates for novel non-messenger RNAs
By generating a specialised cDNA library from four different developmental stages of Drosophila melanogaster, we have identi®ed 66 candidates for small non-messenger RNAs (snmRNAs) and have con®rmed their expression by northern blot analysis. Thirteen of them were expressed at certain stages of D.melanogaster development, only. Thirty®ve species belong to the class of small nucleolar RNAs (snoR...
متن کاملRNomics in Drosophila melanogaster: identification of 66 candidates for novel non-messenger RNAs
By generating a specialised cDNA library from four different developmental stages of Drosophila melanogaster, we have identified 66 candidates for small non-messenger RNAs (snmRNAs) and have confirmed their expression by northern blot analysis. Thirteen of them were expressed at certain stages of D.melanogaster development, only. Thirty-five species belong to the class of small nucleolar RNAs (...
متن کامل