Evolutionary Origins of Pseudogenes and Their Association with Regulatory Sequences in Plants
Evolutionary Origins of Pseudogenes and Their Association with Regulatory Sequences in Plants
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假基因的进化起源及其与植物调控序列的关联
DOI：
10.1105/tpc.18.00601
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发表时间：
2019-03-01
期刊：
影响因子：
11.6
通讯作者：
Zhang, Deqiang
中科院分区：
文献类型：
--
作者：
Xie, Jianbo;Li, Ying;Zhang, Deqiang
假基因(Psi S)，功能基因的无功能近亲，通过复制或逆转座子形成，通过使突变失效而丧失基因功能。进化分析为PSI的起源和对基因调控的影响提供了线索。然而，对植物Psi S的系统研究很少，这阻碍了比较分析。在这里，我们研究了Psi S的起源、进化和在七种被子植物中的表达模式及其与非编码序列的关系。我们鉴定了与250,000个Psi S相似的基因，其中大多数比蛋白质编码基因更具谱系特异性。Psi S在染色体上的分布表明，基因组重组可能有助于Psi的消除。大多数Psi S在序列和表达水平方面进化迅速，表现出组织或阶段特异性的表达模式。我们发现，令人惊讶的是，很大一部分非转座元件调控的非编码RNAs(microRNAs和长非编码RNAs)来自Psi近端上游区域的转录。我们还发现转录因子结合位点优先出现在假定的Psi近端上游区域，而不是随机的基因间隔区，这表明Psi S通过提供转录因子结合位点作为启动子和增强子来调节基因组进化。因此，我们认为Psi转录调节区的快速重新连接是驱动新调节模块起源的主要机制。
Pseudogenes (Psi s), nonfunctional relatives of functional genes, form by duplication or retrotransposition, and loss of gene function by disabling mutations. Evolutionary analysis provides clues to Psi origins and effects on gene regulation. However, few systematic studies of plant Psi s have been conducted, hampering comparative analyses. Here, we examined the origin, evolution, and expression patterns of Psi s and their relationships with noncoding sequences in seven angiosperm plants. We identified similar to 250,000 Psi s, most of which are more lineage specific than protein-coding genes. The distribution of Psi s on the chromosome indicates that genome recombination may contribute to Psi elimination. Most Psi s evolve rapidly in terms of sequence and expression levels, showing tissue- or stage-specific expression patterns. We found that a surprisingly large fraction of nontransposable element regulatory noncoding RNAs (microRNAs and long noncoding RNAs) originate from transcription of Psi proximal upstream regions. We also found that transcription factor binding sites preferentially occur in putative Psi proximal upstream regions compared with random intergenic regions, suggesting that Psi s have conditioned genome evolution by providing transcription factor binding sites that serve as promoters and enhancers. We therefore propose that rapid rewiring of Psi transcriptional regulatory regions is a major mechanism driving the origin of novel regulatory modules.