Rogers Rebekah L, Shao Ling, Thornton Kevin R
Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, Charlotte, North Carolina, United States of America.
Ecology and Evolutionary Biology, University of California, Irvine, Irvine, California, United States of America.
PLoS Genet. 2017 May 22;13(5):e1006795. doi: 10.1371/journal.pgen.1006795. eCollection 2017 May.
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.
一种解释串联重复影响的常见假说是，由于拷贝数变化，全基因重复通常会在基因表达上产生累加性变化。在此，我们使用来自雅库布果蝇群体样本的全基因组RNA测序数据来检验这一“基因剂量”假说。我们几乎没有观察到因捕获5'和3'非翻译区的全转录本重复而导致表达变化的证据。在全基因重复中，我们观察到证据表明各拷贝间的剂量共享可能很常见。全基因重复后缺乏表达变化表明，大多数基因受到严格的调控，因此对基因拷贝数的变化不敏感。相反，我们观察到由于调控元件的重排以及通过串联重复产生嵌合结构，导致了表达水平的变化。此外，我们观察到由串联重复产生的30个新生基因结构，其中23个在睾丸中表达。因此，串联重复的价值可能比简单的基因剂量变化更为复杂。串联重复后嵌合基因形成产生的常见调控效应可能解释了它们对基因组进化的贡献。
