Detection of intergenic non-coding RNAs expressed in the main developmental stages in Drosophila melanogaster.
Detection of intergenic non-coding RNAs expressed in the main developmental stages in Drosophila melanogaster.
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DOI：
10.1093/nar/gkp334
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发表时间：
2009-07
影响因子：
14.9
通讯作者：
Long M
中科院分区：
文献类型：
--
作者：
Li Z;Liu M;Zhang L;Zhang W;Gao G;Zhu Z;Wei L;Fan Q;Long M
在果蝇的不同发育阶段，有多少基因间编码的非编码RNA（ncRNA）表达？以前的分析表明，在一个或几个发展阶段的基因间ncRNA的丰富表达。然而，一些报道称ncRNA最近被伪造，并且通常ncRNA检测的假阳性率是未知的。在这份报告中，我们使用逆转录-PCR（RT-PCR），一个更强大的方法，检测ncRNA的基因间区域，在四个主要的发育阶段（6-8小时的胚胎，20-22小时的胚胎，幼虫和成人）表达。我们测试了1027个区域，占所有基因间区域的约10%，并通过RT-PCR检测转录。18342个RT-PCR实验的结果显示，在发育过程中，72.7%的基因间区域存在转录。早期发育阶段似乎与比后期发育阶段更丰富的ncRNA相关。在早期阶段，我们在一式三份的RT-PCR实验中检测到43.6%的编码转录本的基因间区域，估计整个基因组中有5006个基因间区域可能编码ncRNA。我们比较了RT-PCR相关的方法与以前的基于平铺阵列的方法，并观察到后者的方法是不敏感的短ncRNA，特别是小于120 bp的分子。我们测量了所分析的基因组方法的假阳性率，包括RT-PCR和平铺阵列方法。
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.
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通讯作者：
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