Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing
Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing
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DOI：
10.1186/gb-2010-11-7-r78
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发表时间：
2010-01-01
期刊：
影响因子：
12.3
通讯作者：
Cavelier, Lucia
中科院分区：
文献类型：
--
作者：
Wetterbom, Anna;Ameur, Adam;Cavelier, Lucia
背景资料：我们使用深度测序的cDNA从大脑和肝脏，旨在量化已知基因的表达，并确定新的转录regions.Results：使用严格的转录标准，我们确定了12,843表达的基因，与大多数被发现在这两个组织的黑猩猩转录组。我们进一步鉴定了9，826个与注释的外显子、mRNA或EST不重叠的新转录区域。超过80%的新的转录区域映射在已知基因内或附近，并且通过将测序数据与从头剪接预测相结合，我们预测了几个新的转录区域是新的外显子或3'UTR。对于大约350个新的转录区域，相应的DNA序列在人类参考基因组中不存在。RT-PCR进一步验证了五个基因和一个基因间区域中存在新的转录区。最后，我们描述和实验验证了一个推定的新的多外显子基因，属于ATP盒转运基因家族。该基因在人类中似乎没有功能，因为人类基因组中缺少一个外显子。除了新的外显子和UTR之外，新的转录区域也可以源自不同类型的非编码转录物。我们注意到，表达的重复序列和内含子从未剪接的mRNA是特别常见的，在我们的data.Conclusions：我们的研究结果扩展了黑猩猩基因目录与大量的新的外显子和3'UTR，从而支持哺乳动物基因注释尚未完成的观点。
Background: We profile the chimpanzee transcriptome by using deep sequencing of cDNA from brain and liver, aiming to quantify expression of known genes and to identify novel transcribed regions.Results: Using stringent criteria for transcription, we identify 12,843 expressed genes, with a majority being found in both tissues. We further identify 9,826 novel transcribed regions that are not overlapping with annotated exons, mRNAs or ESTs. Over 80% of the novel transcribed regions map within or in the vicinity of known genes, and by combining sequencing data with de novo splice predictions we predict several of the novel transcribed regions to be new exons or 3' UTRs. For approximately 350 novel transcribed regions, the corresponding DNA sequence is absent in the human reference genome. The presence of novel transcribed regions in five genes and in one intergenic region is further validated with RT-PCR. Finally, we describe and experimentally validate a putative novel multi-exon gene that belongs to the ATP-cassette transporter gene family. This gene does not appear to be functional in human since one exon is absent from the human genome. In addition to novel exons and UTRs, novel transcribed regions may also stem from different types of noncoding transcripts. We note that expressed repeats and introns from unspliced mRNAs are especially common in our data.Conclusions: Our results extend the chimpanzee gene catalogue with a large number of novel exons and 3' UTRs and thus support the view that mammalian gene annotations are not yet complete.