Correlated Evolution of Large DNA Fragments in the 3D Genome of Arabidopsis thaliana
Correlated Evolution of Large DNA Fragments in the 3D Genome of Arabidopsis thaliana
复制标题
拟南芥 3D 基因组中大 DNA 片段的相关进化
DOI：
10.1093/molbev/msaa031
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发表时间：
2020
影响因子：
10.7
通讯作者：
Yang Ruolin
中科院分区：
文献类型：
--
作者：
Yan Yubin;Li Zhaohong;Li Ye;Wu Zefeng;Yang Ruolin
在真核生物中，基因组的三维（3D）构象远非随机的，并且这种非随机的染色质组织与基因表达和蛋白质功能密切相关，这是基因的选择性约束和进化速率的两个关键决定因素。然而，在3D基因组中彼此靠近的基因和其他元件是否以协调的方式进化，还没有在任何生物中进行过研究。为了解决这个问题，我们构建了基于高通量染色体构象捕获数据的拟南芥染色质相互作用网络（CIN），并证明了CIN中相邻的大DNA片段确实表现出比随机片段对更相似的多态性水平和进化速率。使用模拟片段之间的线性距离，我们证明了3D染色体组织在观察到的相关进化中发挥了作用。空间相互作用的片段也表现出更相似的突变率和功能限制在编码区和非编码区比随机预期，表明三维邻居之间的相关进化是联合进化力量的结果。39个基因组和表观基因组特征的集合可以解释基因组中遗传多样性和进化速率的大部分差异。此外，对区域序列的进化具有更大影响的特征往往在CIN中的相邻片段之间显示出更高的相似性，这表明表观遗传修饰和染色质组织在确定3D基因组中大DNA片段的相关进化中起着关键作用。
In eukaryotes, the three-dimensional (3D) conformation of the genome is far from random, and this nonrandom chromatin organization is strongly correlated with gene expression and protein function, which are two critical determinants of the selective constraints and evolutionary rates of genes. However, whether genes and other elements that are located close to each other in the 3D genome evolve in a coordinated way has not been investigated in any organism. To address this question, we constructed chromatin interaction networks (CINs) inArabidopsis thalianabased on high-throughput chromosome conformation capture data and demonstrated that adjacent large DNA fragments in the CIN indeed exhibit more similar levels of polymorphism and evolutionary rates than random fragment pairs. Using simulations that account for the linear distance between fragments, we proved that the 3D chromosomal organization plays a role in the observed correlated evolution. Spatially interacting fragments also exhibit more similar mutation rates and functional constraints in both coding and noncoding regions than the random expectations, indicating that the correlated evolution between 3D neighbors is a result of combined evolutionary forces. A collection of 39 genomic and epigenomic features can explain much of the variance in genetic diversity and evolutionary rates across the genome. Moreover, features that have a greater effect on the evolution of regional sequences tend to show higher similarity between neighboring fragments in the CIN, suggesting a pivotal role of epigenetic modifications and chromatin organization in determining the correlated evolution of large DNA fragments in the 3D genome.