染色质重塑剂在染色质的组装中起着基本作用,转录调节,DNA修复来自多种模型生物的染色质重塑剂的CHD家族的生化和功能表征已经表明,这些重塑剂参与了广泛的活动。然而,因为CHD同源物的进化史尚不清楚,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谱系中进化的。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,特别关注引起植物中观察到的不同拷贝的重复时间。动物,和真菌。我们的分析证实,CHD重塑者的三个主要亚家族起源于真核生物的最后一个共同祖先,随后的损失独立发生在不同的谱系中。改进的分类单元采样确定了植物中CHD重塑子的几个亚科,这些亚科在模型植物拟南芥中不存在或高度分歧。尽管脊椎动物中CHD亚家族扩增的时间对应于整个基因组复制事件,陆地植物CHD多样化的潜在机制似乎更加复杂。蛋白质结构域的分析表明,CHD重塑者的多样化伴随着结构域结构的不同转变,有助于这些重塑者之间观察到的功能差异。这项研究证明了在研究古代进化事件时适当分类单元采样的重要性,以防止对随后的谱系特异性变化的误解,并为整个真核生物中这一关键染色质重塑家族的功能和比较分析提供了一个进化框架。
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.