Tandem duplications lead to novel expression patterns through exon shuffling in <i>Drosophila yakuba</i>

One common hypothesis to explain the impacts of tandem duplications is that whole gene duplications commonly produce additive changes in gene expression due to copy number changes. Here, we use genome wide RNA-seq data from a population sample of Drosophila yakuba to test this ‘gene dosage’ hypothesis. We observe little evidence of expression changes in response to whole transcript duplication capturing 5′ and 3′ UTRs. Among whole gene duplications, we observe evidence that dosage sharing across copies is likely to be common. The lack of expression changes after whole gene duplication suggests that the majority of genes are subject to tight regulatory control and therefore not sensitive to changes in gene copy number. Rather, we observe changes in expression level due to both shuffling of regulatory elements and the creation of chimeric structures via tandem duplication. Additionally, we observe 30 de novo gene structures arising from tandem duplications, 23 of which form with expression in the testes. Thus, the value of tandem duplications is likely to be more intricate than simple changes in gene dosage. The common regulatory effects from chimeric gene formation after tandem duplication may explain their contribution to genome evolution.解释串联重复（tandem duplication）效应的经典假说认为，全基因重复通常会因拷贝数变化引发基因表达的加性改变。本研究借助雅库巴果蝇（Drosophila yakuba）种群样本的全基因组RNA测序（RNA-seq）数据，对这一“基因剂量”假说开展验证。研究未观察到涵盖5'与3'非翻译区（UTR）的全转录本重复会导致显著的基因表达变化。在全基因重复事件中，我们发现拷贝间的剂量共享现象大概率普遍存在。全基因重复后未出现表达变化的结果表明，绝大多数基因受到严格的调控管控，因此对基因拷贝数的改变并不敏感。与之相对，我们观察到基因表达水平的变化源于两类机制：一是调控元件的重排，二是串联重复所介导的嵌合结构形成。此外，本研究发现串联重复可产生30种从头基因结构，其中23种在睾丸中呈现表达活性。由此可见，串联重复的生物学意义远比单纯的基因剂量改变更为复杂精妙。串联重复后嵌合基因形成所带来的普遍调控效应，或可阐释其对基因组进化的贡献。