Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF
Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF
复制标题
使用 Phylo-HMRF 比较多个物种的 3D 基因组组织
DOI：
10.1016/j.cels.2019.05.011
复制
发表时间：
2019
期刊：
影响因子：
9.3
通讯作者：
Ma, Jian
中科院分区：
文献类型：
--
作者：
Yang, Yang;Zhang, Yang;Ren, Bing;Dixon, Jesse R.;Ma, Jian
最近的全基因组染色质相互作用组作图方法提供了新的见解三维基因组组织。然而，我们对哺乳动物3D基因组进化模式的了解仍然有限。特别是，没有现有的基于遗传模型的方法来分析染色质相互作用作为连续特征。在这里，我们开发系统发育隐马尔可夫随机场（Phylo-HMRF），以确定三维基因组的进化模式的基础上，多物种Hi-C数据，共同利用基因组位点和连续性状进化模型之间的空间约束。我们使用Phylo-HMRF来揭示跨物种的3D基因组模式，该模式基于来自四种灵长类动物物种（人类，黑猩猩，倭黑猩猩和大猩猩）中相同细胞类型的Hi-C数据。三维基因组的进化模式与基因组的结构和功能特征相关。这项工作提供了一个新的框架来分析多物种连续的基因组特征与空间约束，并有可能帮助揭示进化的3D基因组组织的原则。
Recent whole-genome mapping approaches for the chromatin interactome have offered new insights into 3D genome organization. However, our knowledge of the evolutionary patterns of 3D genome in mammals remains limited. In particular, there are no existing phylogenetic-model-based methods to analyze chromatin interactions as continuous features. Here, we develop phylogenetic hidden Markov random field (Phylo-HMRF) to identify evolutionary patterns of 3D genome based on multi-species Hi-C data by jointly utilizing spatial constraints among genomic loci and continuous-trait evolutionary models. We used Phylo-HMRF to uncover cross-species 3D genome patterns based on Hi-C data from the same cell type in four primate species (human, chimpanzee, bonobo, and gorilla). The identified evolutionary patterns of 3D genome correlate with features of genome structure and function. This work provides a new framework to analyze multi-species continuous genomic features with spatial constraints and has the potential to help reveal the evolutionary principles of 3D genome organization.