Gain, loss and divergence in primate zinc-finger genes: a rich resource for evolution of gene regulatory differences between species.
Gain, loss and divergence in primate zinc-finger genes: a rich resource for evolution of gene regulatory differences between species.
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DOI：
10.1371/journal.pone.0021553
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发表时间：
2011
期刊：
影响因子：
3.7
通讯作者：
Stubbs L
中科院分区：
文献类型：
--
作者：
Nowick K;Fields C;Gernat T;Caetano-Anolles D;Kholina N;Stubbs L
人类和其他灵长类动物之间主要表型差异背后的分子变化还不清楚，但基因调控的改变可能起着重要作用。在这里，我们进行了彻底的灵长类动物转录因子，Krüppel型锌指（KZNF）基因家族的最大家族的进化分析。我们在三种灵长类动物（黑猩猩、猩猩和恒河猴）中鉴定并策划了KZNF的基因和假基因模型，以便与策划的人类KZNF进行比较。我们表明灵长类KZNF的近期进化历史非常复杂，包括许多谱系特异性重复和缺失。我们发现了213个物种特异性KZNF，其中7个人类特异性基因和23个黑猩猩特异性基因。两个人类特异性基因被实验验证。人类有10个基因丢失，黑猩猩有13个基因丢失，要么是缺失，要么是假基因化。我们还鉴定了30个具有人类特异性的KZNF直系同源物和42个具有黑猩猩特异性序列变化的KZNF直系同源物，这些序列变化预计会影响蛋白质的DNA结合特性。其中11个基因显示出加速进化的特征，表明人类和黑猩猩之间存在正向选择。在灵长类动物进化过程中，最广泛的KZNF库的重塑，包括大多数基因的添加，伪基因化和结构变化发生在人类亚科。使用锌指（ZNF）结合预测，我们认为这些变化对人类基因调控网络的潜在影响。这个TF家族中的巨大物种差异与灵长类基因组的整体高度保守性形成鲜明对比，并可能代表灵长类进化的有力驱动力。
The molecular changes underlying major phenotypic differences between humans and other primates are not well understood, but alterations in gene regulation are likely to play a major role. Here we performed a thorough evolutionary analysis of the largest family of primate transcription factors, the Krüppel-type zinc finger (KZNF) gene family. We identified and curated gene and pseudogene models for KZNFs in three primate species, chimpanzee, orangutan and rhesus macaque, to allow for a comparison with the curated set of human KZNFs. We show that the recent evolutionary history of primate KZNFs has been complex, including many lineage-specific duplications and deletions. We found 213 species-specific KZNFs, among them 7 human-specific and 23 chimpanzee-specific genes. Two human-specific genes were validated experimentally. Ten genes have been lost in humans and 13 in chimpanzees, either through deletion or pseudogenization. We also identified 30 KZNF orthologs with human-specific and 42 with chimpanzee-specific sequence changes that are predicted to affect DNA binding properties of the proteins. Eleven of these genes show signatures of accelerated evolution, suggesting positive selection between humans and chimpanzees. During primate evolution the most extensive re-shaping of the KZNF repertoire, including most gene additions, pseudogenizations, and structural changes occurred within the subfamily homininae. Using zinc finger (ZNF) binding predictions, we suggest potential impact these changes have had on human gene regulatory networks. The large species differences in this family of TFs stands in stark contrast to the overall high conservation of primate genomes and potentially represents a potent driver of primate evolution.
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影响因子：
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