Detection and evaluation of intron retention events in the human transcriptome
Detection and evaluation of intron retention events in the human transcriptome
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DOI：
10.1261/rna.5123504
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发表时间：
2004-05-01
期刊：
影响因子：
4.5
通讯作者：
De Souza, SJ
中科院分区：
文献类型：
--
作者：
Galante, PAF;Sakabe, NJ;De Souza, SJ
选择性剪接是人类转录组中一种非常常见的现象。选择性剪接主要有四种类型：外显子跳跃、选择性3‘剪接点、选择性5’剪接点和内含子保留。在这里，我们提出了一组21,106个已知人类基因中内含子保留的大规模分析。我们观察到，这些基因中有14.8%显示出至少一个内含子保留事件的证据。大多数事件位于人类转录本的非翻译区(UTRs)内。对于那些干扰编码区的保留内含子，GC含量、密码子使用和终止密码子的频率表明这些序列处于编码潜力的选择之下。此外，编码区内26%的内含子参与蛋白质结构域的编码。与小鼠的比较表明，在所有人类保留内含子的信息示例中，至少有22%也存在于小鼠转录组中。我们讨论到，我们提供的数据表明，很大一部分观察到的事件并不是虚假的，可能反映了生物学意义。这些分析还使我们能够产生一组可靠的内含子保留事件，可用于识别剪接调控元件。
Alternative splicing is a very frequent phenomenon in the human transcriptome. There are four major types of alternative splicing: exon skipping, alternative 3' splice site, alternative 5' splice site, and intron retention. Here we present a large-scale analysis of intron retention in a set of 21,106 known human genes. We observed that 14.8% of these genes showed evidence of at least one intron retention event. Most of the events are located within the untranslated regions (UTRs) of human transcripts. For those retained introns interrupting the coding region, the GC content, codon usage, and the frequency of stop codons suggest that these sequences are under selection for coding potential. Furthermore, 26% of the introns within the coding region participate in the coding of a protein domain. A comparison with mouse shows that at least 22% of all informative examples of retained introns in human are also present in the mouse transcriptome. We discuss that the data we present suggest that a significant fraction of the observed events is not spurious and might reflect biological significance. The analyses also allowed us to generate a reliable set of intron retention events that can be used for the identification of splicing regulatory elements.