Detecting novel low-abundant transcripts in Drosophila
Detecting novel low-abundant transcripts in Drosophila
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作者：
Lee, S;Bao, JY;Wang, SM
越来越多的证据表明，低丰度转录本可能在生物过程中发挥重要作用。为了估计低丰度转录本在真核基因组中的流行程度，我们使用SAGE技术在果蝇中进行了转录组分析。我们从果蝇胚胎、幼虫、蛹、成虫和睾丸组织中表达的转录本中收集了244，313个SAGE标签。从这些SAGE标签中，我们识别出40，823个独特的SAGE标签。我们的分析表明，40，823个独特的SAGE标签中有55%是新的，在目前已知的果蝇转录本中没有匹配，并且大多数新的SAGE标签具有低拷贝数。进一步分析表明，这些新型SAGE标签代表了从目前注释的外显子之外的基因座表达的新型低丰度转录本，包括基因间区和内含子区，以及果蝇基因组中目前注释的外显子的反义。我们的研究揭示了大量的新的低丰度转录本在果蝇中的存在，并强调需要分离这些新的低丰度转录本进行进一步的生物学研究。
Increasing evidence suggests that low-abundant transcripts may play fundamental roles in biological processes. In an attempt to estimate the prevalence of low-abundant transcripts in eukaryotic genomes, we performed a transcriptome analysis in Drosophila using the SAGE technique. We collected 244,313 SAGE tags from transcripts expressed in Drosophila embryonic, larval, pupae, adult, and testicular tissue. From these SAGE tags, we identified 40,823 unique SAGE tags. Our analysis showed that 55 % of the 40,823 unique SAGE tags are novel without matches in currently known Drosophila transcripts, and most of the novel SAGE tags have low copy numbers. Further analysis indicated that these novel SAGE tags represent novel low-abundant transcripts expressed from loci outside of currently annotated exons including the intergenic and intronic regions, and antisense of the currently annotated exons in the Drosophila genome. Our study reveals the presence of a significant number of novel low-abundant transcripts in Drosophila, and highlights the need to isolate these novel low-abundant transcripts for further biological studies.