Genome-wide maps of ribosomal occupancy provide insights into adaptive evolution and regulatory roles of uORFs during Drosophila development.
Genome-wide maps of ribosomal occupancy provide insights into adaptive evolution and regulatory roles of uORFs during Drosophila development.
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核糖体占据的全基因组图谱提供了对果蝇发育过程中 uORF 的适应性进化和调节作用的见解。
DOI：
10.1371/journal.pbio.2003903
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发表时间：
2018-07
期刊：
影响因子：
9.8
通讯作者：
Lu J
中科院分区：
文献类型：
--
作者：
Zhang H;Dou S;He F;Luo J;Wei L;Lu J
上游开放阅读框（uORFs）通过翻译抑制对主要编码DNA序列（CDS）的调控起重要作用。尽管它们在基因组中普遍存在，但uORF总体上受到自然选择的歧视。然而，目前还不清楚为什么在基因组中有这么多的uORF比中性进化假设下预期的更保守。在这里，我们产生了全基因组的翻译效率（TE）在整个生命周期的果蝇的密码子水平的地图。我们鉴定了35，735个表达的uORF，其中32，224个（90.2%）显示了果蝇发育期间核糖体占据的证据。uORF的核糖体占有率由基因组特征决定，例如其起始密码子周围的优化序列环境、与CDS的较短距离以及较高的编码潜力。我们的群体基因组分析表明，产生或破坏uORF的分离突变在D.黑腹菌然而，我们首次发现，许多（68.3%）新固定的uORF与核糖体在D。是由达尔文的正选择所驱动的。我们的研究结果还表明，uORF在控制果蝇的翻译程序中起着至关重要的作用。此外，我们发现，许多uORF的转录或翻译在一个发展阶段，性别，或组织特异性的方式，这表明，选择性转录或翻译的uORF可能潜在的调节TE的下游CDS在果蝇的发展。信使RNA的5′非翻译区（UTR）上游的开放阅读框（uORF）可以通过隔离核糖体来抑制下游蛋白质编码区的翻译。此外，已知破坏现有uORF或产生新uORF的突变会导致人类疾病。虽然产生新的uORF的突变通常是有害的，并且被选择反对，但许多uORF在真核物种中进化保守。为了解决这一难题，我们使用了广泛的mRNA-Seq和核糖体分析来生成果蝇D生命周期中核糖体占用和翻译效率（TE）的高分辨率全基因组图谱。黑腹菌这使我们能够确定影响其与核糖体结合能力的uORF的序列特征。我们首次证明，大多数新固定的uORF在D。黑腹果蝇，特别是翻译的果蝇，都处于正达尔文选择的作用下。我们还表明，uORF对下游蛋白编码区的翻译产生广泛的抑制作用。我们发现，许多uORF的转录或翻译的发展阶段，性别，或组织特异性的方式。我们的研究结果表明，在果蝇发育过程中，TE的uORF的变化，以及列入/排除uORF，经常利用反向影响下游蛋白质编码区的翻译。我们的研究提供了新的见解uORF介导的调节的分子机制和功能后果。
Upstream open reading frames (uORFs) play important roles in regulating the main coding DNA sequences (CDSs) via translational repression. Despite their prevalence in the genomes, uORFs are overall discriminated against by natural selection. However, it remains unclear why in the genomes there are so many uORFs more conserved than expected under the assumption of neutral evolution. Here, we generated genome-wide maps of translational efficiency (TE) at the codon level throughout the life cycle of Drosophila melanogaster. We identified 35,735 uORFs that were expressed, and 32,224 (90.2%) of them showed evidence of ribosome occupancy during Drosophila development. The ribosome occupancy of uORFs is determined by genomic features, such as optimized sequence contexts around their start codons, a shorter distance to CDSs, and higher coding potentials. Our population genomic analysis suggests the segregating mutations that create or disrupt uORFs are overall deleterious in D. melanogaster. However, we found for the first time that many (68.3% of) newly fixed uORFs that are associated with ribosomes in D. melanogaster are driven by positive Darwinian selection. Our findings also suggest that uORFs play a vital role in controlling the translational program in Drosophila. Moreover, we found that many uORFs are transcribed or translated in a developmental stage-, sex-, or tissue-specific manner, suggesting that selective transcription or translation of uORFs could potentially modulate the TE of the downstream CDSs during Drosophila development. Upstream open reading frames (uORFs) in the 5′ untranslated regions (UTRs) of messenger RNAs can potentially inhibit translation of the downstream regions that encode proteins by sequestering protein-making machinery the ribosome. Moreover, mutations that destroy existing uORFs or create new ones are known to cause human disease. Although mutations that create new uORFs are generally deleterious and are selected against, many uORFs are evolutionarily conserved across eukaryotic species. To resolve this dilemma, we used extensive mRNA-Seq and ribosome profiling to generate high-resolution genome-wide maps of ribosome occupancy and translational efficiency (TE) during the life cycle of the fruit fly D. melanogaster. This allowed us to identify the sequence features of uORFs that influence their ability to associate with ribosomes. We demonstrate for the first time that the majority of the newly fixed uORFs in D. melanogaster, especially the translated ones, are under positive Darwinian selection. We also show that uORFs exert widespread repressive effects on the translation of the downstream protein-coding region. We find that many uORFs are transcribed or translated in a developmental stage-, sex-, or tissue-specific manner. Our results suggest that during Drosophila development, changes in the TE of uORFs, as well as the inclusion/exclusion of uORFs, are frequently exploited to inversely influence the translation of the downstream protein-coding regions. Our study provides novel insights into the molecular mechanisms and functional consequences of uORF-mediated regulation.
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