CHD Chromatin Remodeling Protein Diversification Yields Novel Clades and Domains Absent in Classic Model Organisms.
CHD Chromatin Remodeling Protein Diversification Yields Novel Clades and Domains Absent in Classic Model Organisms.
复制标题
CHD染色质重塑蛋白的多样化产生了经典模式生物所没有的新的分支和结构域。
DOI：
10.1093/gbe/evac066
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发表时间：
2022-05-03
影响因子：
3.3
通讯作者：
Wisecaver, Jennifer H.
中科院分区：
文献类型：
--
作者：
Trujillo, Joshua T.;Long, Jiaxin;Aboelnour, Erin;Ogas, Joseph;Wisecaver, Jennifer H.
关键词：
染色质重塑在染色质的组装、转录调控和DNA修复中起着重要作用。来自各种模式生物的CHD染色质重塑家族的生物化学和功能表征表明，这些重塑参与广泛的活动。然而，由于CHD同源物的进化历史尚不清楚，因此很难预测这些活动中哪些是广泛保守的，哪些是最近在单个真核细胞谱系中进化的。在这里，我们对来自1，894个物种的8，042个CHD同源物进行了全面的系统发育分析，以创建该家族在真核生物中进化的模型，特别关注在植物，动物和真菌中观察到的不同拷贝的复制时间。我们的分析证实，CHD重塑的三个主要亚家族起源于真核生物的最后一个共同祖先，随后的损失独立地发生在不同的谱系。改进的分类群取样鉴定了CHD重塑植物中的几个亚科，这些亚科在模式植物拟南芥中不存在或高度分化。而CHD亚科在脊椎动物中的扩展时间对应于全基因组复制事件，CHD多样化的机制在陆地植物中出现更复杂。蛋白质结构域的分析表明，CHD重塑多样化一直伴随着结构域结构的明显转变，有助于这些重塑之间观察到的功能差异。这项研究表明，在研究古代进化事件，以防止随后的谱系特异性变化的误解时，适当的分类单元采样的重要性，并提供了一个进化框架，跨真核生物的这个关键的染色质重塑家族的功能和比较分析。
Chromatin remodelers play a fundamental role in the assembly of chromatin, regulation of transcription, and DNA repair. Biochemical and functional characterizations of the CHD family of chromatin remodelers from a variety of model organisms have shown that these remodelers participate in a wide range of activities. However, because the evolutionary history of CHD homologs is unclear, it is difficult to predict which of these activities are broadly conserved and which have evolved more recently in individual eukaryotic lineages. Here, we performed a comprehensive phylogenetic analysis of 8,042 CHD homologs from 1,894 species to create a model for the evolution of this family across eukaryotes with a particular focus on the timing of duplications that gave rise to the diverse copies observed in plants, animals, and fungi. Our analysis confirms that the three major subfamilies of CHD remodelers originated in the eukaryotic last common ancestor, and subsequent losses occurred independently in different lineages. Improved taxon sampling identified several subfamilies of CHD remodelers in plants that were absent or highly divergent in the model plant Arabidopsis thaliana. Whereas the timing of CHD subfamily expansions in vertebrates corresponds to whole genome duplication events, the mechanisms underlying CHD diversification in land plants appear more complicated. Analysis of protein domains reveals that CHD remodeler diversification has been accompanied by distinct transitions in domain architecture, contributing to the functional differences observed between these remodelers. This study demonstrates the importance of proper taxon sampling when studying ancient evolutionary events to prevent misinterpretation of subsequent lineage-specific changes and provides an evolutionary framework for functional and comparative analysis of this critical chromatin remodeler family across eukaryotes.
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影响因子：
5.6
作者：
Allen, Mark D.;Religa, Tomasz L.;Bycroft, Mark
通讯作者：
Bycroft, Mark
影响因子：
10.5
作者：
Alendar A;Berns A
通讯作者：
Berns A
影响因子：
3.5
作者：
Bosman, EA;Penn, AC;Steel, KP
通讯作者：
Steel, KP
DOI：
10.1073/pnas.1420657112
发表时间：
2015-02-17
影响因子：
11.1
作者：
Derelle, Romain;Torruella, Guifre;Elias, Marek
通讯作者：
Elias, Marek
影响因子：
3.3
作者：
Carter, Benjamin;Henderson, James T.;Ogas, Joe
通讯作者：
Ogas, Joe