Department of Plant and Microbial Biology, University of Zurich, Switzerland.
Eur J Cell Biol. 2023 Dec;102(4):151344. doi: 10.1016/j.ejcb.2023.151344. Epub 2023 Aug 1.
Research on the three-dimensional (3D) structure of the genome and its distribution within the nuclear space has made a big leap in the last two decades. Work in the animal field has led to significant advances in our general understanding on eukaryotic genome organization. This did not only bring along insights into how the 3D genome interacts with the epigenetic landscape and the transcriptional machinery but also how 3D genome architecture is relevant for fundamental developmental processes, such as cell differentiation. In parallel, the 3D organization of plant genomes have been extensively studied, which resulted in both congruent and novel findings, contributing to a more complete view on how eukaryotic genomes are organized in multiple dimensions. Plant genomes are remarkably diverse in size, composition, and ploidy. Furthermore, as intrinsically sessile organisms without the possibility to relocate to more favorable environments, plants have evolved an elaborate epigenetic repertoire to rapidly respond to environmental challenges. The diversity in genome organization and the complex epigenetic programs make plants ideal study subjects to acquire a better understanding on universal features and inherent constraints of genome organization. Furthermore, considering a wide range of species allows us to study the evolutionary crosstalk between the various levels of genome architecture. In this article, we aim at summarizing important findings on 3D genome architecture obtained in various plant species. These findings cover many aspects of 3D genome organization on a wide range of levels, from gene loops to topologically associated domains and to global 3D chromosome configurations. We present an overview on plant 3D genome organizational features that resemble those in animals and highlight facets that have only been observed in plants to date.
在过去的二十年中，对基因组的三维（3D）结构及其在核空间内分布的研究取得了重大飞跃。动物领域的工作使我们对真核基因组组织有了更深入的了解。这不仅使我们对 3D 基因组如何与表观遗传景观和转录机制相互作用有了更深入的了解，也使我们对 3D 基因组结构如何与基本发育过程（如细胞分化）相关有了更深入的了解。与此同时，植物基因组的 3D 组织也得到了广泛的研究，这些研究既有一致的发现，也有新颖的发现，为我们提供了一个更完整的视图，了解真核基因组是如何在多个维度上组织的。植物基因组在大小、组成和倍性方面差异很大。此外，作为没有可能迁移到更有利环境的固有固着生物，植物已经进化出了复杂的表观遗传机制，以快速应对环境挑战。基因组组织的多样性和复杂的表观遗传程序使植物成为研究的理想对象，有助于更好地理解基因组组织的普遍特征和内在约束。此外，考虑到广泛的物种，我们可以研究不同层次的基因组结构之间的进化相互作用。在本文中，我们旨在总结在各种植物物种中获得的关于 3D 基因组结构的重要发现。这些发现涵盖了从基因环到拓扑关联域和全局 3D 染色体构象等多个水平上的 3D 基因组组织的许多方面。我们介绍了植物 3D 基因组组织特征的概述，这些特征类似于动物中的特征，并强调了迄今为止仅在植物中观察到的特征。
