Rapid Cis-Trans Coevolution Driven by a Novel Gene Retroposed from a Eukaryotic Conserved CCR4-NOT Component in Drosophila.
Rapid Cis-Trans Coevolution Driven by a Novel Gene Retroposed from a Eukaryotic Conserved CCR4-NOT Component in Drosophila.
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果蝇CCR 4-NOT真核保守区基因的快速顺反协同进化
DOI：
10.3390/genes13010057
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发表时间：
2021-12-26
期刊：
影响因子：
3.5
通讯作者：
Long M
中科院分区：
文献类型：
--
作者：
Krinsky BH;Arthur RK;Xia S;Sosa D;Arsala D;White KP;Long M
年轻的或新进化的基因在生命之树中无处不在，它们可以迅速获得影响各种生物过程的新功能。以前的工作确定了一个年轻的调节重复基因在果蝇，宙斯，出乎意料地迅速从它的父母，Caf 40，一个非常保守的组成部分，在CCR 4-NOT机制在转录后和翻译后调节真核细胞，并承担在男性生殖系统中的角色。这种新功能化伴随着宙斯蛋白与整个果蝇基因组的位点的差异结合。然而，新的DNA结合蛋白获得并与基因组中的靶标共同进化的方式尚不清楚。通过比较来自D. melanogaster和D. simulans与D. yakuba，一个物种，分歧之前的复制事件，我们发现了一个动态模式，其中宙斯绑定迅速协同进化与以前未知的DNA基序，我们称之为Caf 40和宙斯相关的基序（CAZAM），积极选择的影响下。有趣的是，虽然两个宙斯拷贝都获得了男性偏好和睾丸特异性基因的靶点，但D。melanogaster和D. simulans蛋白质在不同的染色体上有专门的结合，这种模式在相关基序的进化中得到了回应。利用CRISPR-Cas9介导的Zeus基因敲除和RNA-Seq，我们发现Zeus调控了661个差异表达基因（DEG）的表达。我们的研究结果表明，年轻的调控基因的进化可以耦合到大量的重新布线的转录网络，他们整合，即使在很短的进化时间尺度。因此，我们的研究结果揭示了与新基因相关的动态全基因组进化过程。
Young, or newly evolved, genes arise ubiquitously across the tree of life, and they can rapidly acquire novel functions that influence a diverse array of biological processes. Previous work identified a young regulatory duplicate gene in Drosophila, Zeus that unexpectedly diverged rapidly from its parent, Caf40, an extremely conserved component in the CCR4–NOT machinery in post-transcriptional and post-translational regulation of eukaryotic cells, and took on roles in the male reproductive system. This neofunctionalization was accompanied by differential binding of the Zeus protein to loci throughout the Drosophila melanogaster genome. However, the way in which new DNA-binding proteins acquire and coevolve with their targets in the genome is not understood. Here, by comparing Zeus ChIP-Seq data from D. melanogaster and D. simulans to the ancestral Caf40 binding events from D. yakuba, a species that diverged before the duplication event, we found a dynamic pattern in which Zeus binding rapidly coevolved with a previously unknown DNA motif, which we term Caf40 and Zeus-Associated Motif (CAZAM), under the influence of positive selection. Interestingly, while both copies of Zeus acquired targets at male-biased and testis-specific genes, D. melanogaster and D. simulans proteins have specialized binding on different chromosomes, a pattern echoed in the evolution of the associated motif. Using CRISPR-Cas9-mediated gene knockout of Zeus and RNA-Seq, we found that Zeus regulated the expression of 661 differentially expressed genes (DEGs). Our results suggest that the evolution of young regulatory genes can be coupled to substantial rewiring of the transcriptional networks into which they integrate, even over short evolutionary timescales. Our results thus uncover dynamic genome-wide evolutionary processes associated with new genes.
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DOI：
10.1093/bioinformatics/btr064
发表时间：
2011-04-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Grant CE;Bailey TL;Noble WS
通讯作者：
Noble WS
影响因子：
7
作者：
Arthur RK;Ma L;Slattery M;Spokony RF;Ostapenko A;Nègre N;White KP
通讯作者：
White KP
影响因子：
4.8
作者：
Bassett, Andrew;Liu, Ji-Long
通讯作者：
Liu, Ji-Long
DOI：
10.1073/pnas.0503528102
发表时间：
2005-08-09
影响因子：
11.1
作者：
Jones, CD;Begun, DJ
通讯作者：
Begun, DJ
影响因子：
5.6
作者：
Chen, JJ;Rappsilber, J;Denis, CL
通讯作者：
Denis, CL