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.**背景**：长度非3的倍数（non-3n）、长度≤100碱基对的小插入缺失（insertions and deletions, indels）在蛋白质编码序列中受到强烈选择约束且丰度显著降低。这类选择约束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'UTR）中，上游起始密码子（upstream start codons, uAUG）与上游开放阅读框（upstream open reading frames, uORF）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，自然选择会不利于5'UTR中出现non-3n indels。 **结果**：我们设计了插入缺失选择指数（Indel Selection Index），用于量化5'UTR中non-3n indels所受的选择约束。该指数可校正所分析5'UTR的基因组组成特征，并可衡量uAUG下游non-3n indels发生耗竭的概率。通过比对人鼠同源基因的实验验证转录本，我们发现两类uAUG（可变翻译起始位点，以及与编码序列重叠的uORF的uAUG）下游的non-3n indels均占比显著偏低。无论序列比对工具、人鼠基因结构差异，抑或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。 **结论**：据我们所知，本研究首次证实了5'UTR中non-3n indels受到选择约束。这类约束可能与uAUG/uORF在翻译调控中的功能，或蛋白质异构体的生成相关。本研究因此为哺乳动物5'UTR的演化研究提供了全新视角。