Data from: Exploring the selective constraint on the sizes of insertions and deletions in 5’ untranslated regions in mammals

Background: 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. Results: 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. Conclusions: 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.

研究背景：长度非3的整倍数（non-3n）、长度≤100 bp的小插入缺失（insertions and deletions，简称indels）在蛋白质编码序列中受到强烈的选择限制并发生耗竭。此类选择限制此前从未在非编码基因组区域中被报道过。在哺乳动物基因组的5'非翻译区（5'untranslated regions, 5'UTRs）中，上游起始密码子（upstream start codons, uAUGs）与上游开放阅读框（upstream open reading frames, uORFs）可调控蛋白质翻译过程。若上游开放阅读框中存在non-3n indels，则可能破坏这些调控元件的功能。据此我们提出假说：当此类调控元件存在时，自然选择会对5'UTRs中的non-3n indels产生排斥作用。

研究结果：本研究设计了插入缺失选择指数（Indel Selection Index），用于量化5'UTRs中non-3n indels所受的选择限制。该指数针对所分析的5'UTRs的基因组组成进行校正，并可量化上游起始密码子下游non-3n indels发生耗竭的概率。通过比对经实验验证的人-鼠同源基因转录本，本研究证实两类上游起始密码子（可变翻译起始位点、与编码序列重叠的上游开放阅读框的上游起始密码子）下游的non-3n indels丰度显著偏低。无论比对工具、人-鼠基因结构差异，或是分析所用可变剪接异构体的筛选标准如何，该结果均保持稳健。

研究结论：据我们所知，本研究首次证实5'UTRs中的non-3n indels受到选择限制。此类选择限制可能与上游起始密码子/上游开放阅读框在翻译调控或蛋白质异构体生成中的调控功能相关。因此，本研究为哺乳动物5'UTRs的进化研究提供了全新视角。