Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, 350 Taiwan.
BMC Evol Biol. 2011 Jul 5;11:192. doi: 10.1186/1471-2148-11-192.
Small insertions and deletions ("indels" with size >/= 100 bp) whose lengths are not multiples of three (non-3n) are strongly constrained and depleted in protein-coding sequences. Such a constraint has never been reported in noncoding genomic regions. In 5'untranslated regions (5'UTRs) in mammalian genomes, upstream start codons (uAUGs) and upstream open reading frames (uORFs) can regulate protein translation. The presence of non-3n indels in uORFs can potentially disrupt the functions of these regulatory elements. We thus hypothesize that natural selection disfavors non-3n indels in 5'UTRs when these regulatory elements are present.
We design the Indel Selection Index to measure the selective constraint on non-3n indels in 5'UTRs. The index controls for the genomic compositions of the analyzed 5'UTRs and measures the probability of non-3n indel depletion downstream of uAUGs. By comparing the experimentally supported transcripts of human-mouse orthologous genes, we demonstrate that non-3n indels downstream of two types of uAUGs (alternative translation initiation sites and the uAUGs of coding sequence-overlapping uORFs) are underrepresented. The results hold well regardless of differences in alignment tool, gene structures between human and mouse, or the criteria in selecting alternatively spliced isoforms used for the analysis.
To our knowledge, this is the first study to demonstrate selective constraints on non-3n indels in 5'UTRs. Such constraints may be associated with the regulatory functions of uAUGs/uORFs in translational regulation or the generation of protein isoforms. Our study thus brings a new perspective to the evolution of 5'UTRs in mammals.
长度不是三的倍数（非 3n）的小插入和缺失（“indels”）在蛋白质编码序列中受到强烈限制和匮乏。这种限制在非编码基因组区域从未有过报道。在哺乳动物基因组的 5'非翻译区（5'UTRs）中，上游起始密码子（uAUGs）和上游开放阅读框（uORFs）可以调节蛋白质翻译。uORFs 中非 3n 的 indels 的存在可能会破坏这些调节元件的功能。因此，我们假设当这些调节元件存在时，自然选择不利于 5'UTRs 中非 3n 的 indels。
我们设计了 Indel Selection Index 来衡量 5'UTRs 中非 3n indels 的选择约束。该指数控制了分析的 5'UTRs 的基因组组成，并测量了 uAUG 下游非 3n indel 匮乏的概率。通过比较人类-鼠同源基因的实验支持的转录本，我们证明了两种类型的 uAUG （替代翻译起始位点和编码序列重叠的 uORFs 的 uAUG）下游的非 3n indels 代表性不足。无论用于分析的人类和鼠基因结构的对齐工具、差异，或选择替代剪接异构体的标准如何，结果都保持不变。
据我们所知，这是第一项证明 5'UTRs 中非 3n indels 存在选择约束的研究。这种约束可能与 uAUGs/uORFs 在翻译调节或蛋白质同工型产生中的调节功能有关。因此，我们的研究为哺乳动物 5'UTRs 的进化带来了新的视角。
