Intron size, abundance, and distribution within untranslated regions of genes
Intron size, abundance, and distribution within untranslated regions of genes
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DOI：
10.1093/molbev/msl111
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发表时间：
2006-12-01
影响因子：
10.7
通讯作者：
Lynch, Michael
中科院分区：
文献类型：
--
作者：
Hong, Xin;Scofield, Douglas G.;Lynch, Michael
大多数有关内含子进化的研究主要考虑编码序列（CDS）内的内含子，而不考虑位于基因非翻译区（UTR）内的内含子。在这里，我们使用拟南芥、果蝇、人类和小鼠这四个物种的全长 cDNA 文库和完整基因组序列直接确定了基因 UTR 中的内含子大小、丰度和分布。 5' UTR 中的总体内含子占用率（内含子/外显子 kbp）低于 CDS，但 5' UTR 中的内含子密度（包含内含子的区域中的内含子占用率）往往高于 CDS。 5' UTR 中的内含子大约是 CDS 中内含子的两倍，并且 5' UTR-CDS 边界处的内含子大小急剧下降。我们对 5'UTR 中较大内含子大小的选择的存在提出了机械解释，并概述了该假设的几个含义。我们发现内含子随机分布在 5' UTR 内，只要假定所需的最小外显子大小。 3' UTR 中的内含子数量远低于 5' UTR 中的内含子。虽然这对于具有内含子依赖性无义介导的衰变 (NMD) 途径的人类和小鼠来说是预期的，这些途径会阻碍 3'UTR 内内含子的存在，但对于可能缺乏内含子依赖性 NMD 的拟南芥和黑腹果蝇来说也是如此。我们的发现对内含子进化和一般基因组进化理论具有多种意义。
Most research concerning the evolution of introns has largely considered introns within coding sequences (CDSs), without regard for introns located within untranslated regions (UTRs) of genes. Here, we directly determined intron size, abundance, and distribution in UTRs of genes using full-length cDNA libraries and complete genome sequences for four species, Arabidopsis thaliana, Drosophila melanogaster, human, and mouse. Overall intron occupancy (introns/exon kbp) is lower in 5' UTRs than CDSs, but intron density (intron occupancy in regions containing introns) tends to be higher in 5' UTRs than in CDSs. Introns in 5' UTRs are roughly twice as large as introns in CDSs, and there is a sharp drop in intron size at the 5' UTR-CDS boundary. We propose a mechanistic explanation for the existence of selection for larger intron size in 5' UTRs, and outline several implications of this hypothesis. We found introns to be randomly distributed within 5' UTRs, so long as a minimum required exon size was assumed. Introns in 3' UTRs were much less abundant than in 5' UTRs. Though this was expected for human and mouse that have intron-dependent nonsense-mediated decay (NMD) pathways that discourage the presence of introns within the 3' UTR, it was also true for A. thaliana and D. melanogaster, which may lack intron-dependent NMD. Our findings have several implications for theories of intron evolution and genome evolution in general.