Szalay Michael-Florian, Majchrzycka Blanka, Jerković Ivana, Cavalli Giacomo, Ibrahim Daniel M
Institute of Human Genetics, CNRS and Univ. Montpellier, Montpellier, France.
Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Center for Regenerative Therapies, Berlin, Germany.
Nat Struct Mol Biol. 2024 Dec;31(12):1824-1837. doi: 10.1038/s41594-024-01427-y. Epub 2024 Nov 26.
The genome of all organisms is spatially organized to function efficiently. The advent of genome-wide chromatin conformation capture (Hi-C) methods has revolutionized our ability to probe the three-dimensional (3D) organization of genomes across diverse species. In this Review, we compare 3D chromatin folding from bacteria and archaea to that in mammals and plants, focusing on topology at the level of gene regulatory domains. In doing so, we consider systematic similarities and differences that hint at the origin and evolution of spatial chromatin folding and its relation to gene activity. We discuss the universality of spatial chromatin domains in all kingdoms, each encompassing one to several genes. We also highlight differences between organisms and suggest that similar features in Hi-C matrices do not necessarily reflect the same biological process or function. Furthermore, we discuss the evolution of domain boundaries and boundary-forming proteins, which indicates that structural maintenance of chromosome (SMC) proteins and the transcription machinery are the ancestral sculptors of the genome. Architectural proteins such as CTCF serve as clade-specific determinants of genome organization. Finally, studies in many non-model organisms show that, despite the ancient origin of 3D chromatin folding and its intricate link to gene activity, evolution tolerates substantial changes in genome organization.
所有生物体的基因组都在空间上进行了组织，以实现高效运作。全基因组染色质构象捕获（Hi-C）方法的出现，彻底改变了我们探究不同物种基因组三维（3D）组织的能力。在本综述中，我们比较了细菌、古菌与哺乳动物和植物的三维染色质折叠情况，重点关注基因调控域水平的拓扑结构。在此过程中，我们考虑了系统的异同点，这些异同点暗示了空间染色质折叠的起源和进化及其与基因活性的关系。我们讨论了所有生物界中空间染色质结构域的普遍性，每个结构域包含一到几个基因。我们还强调了不同生物体之间的差异，并指出Hi-C矩阵中的相似特征不一定反映相同的生物学过程或功能。此外，我们讨论了结构域边界和边界形成蛋白的进化，这表明染色体结构维持（SMC）蛋白和转录机制是基因组的原始塑造者。诸如CTCF等结构蛋白作为基因组组织的特定进化枝决定因素。最后，对许多非模式生物的研究表明，尽管三维染色质折叠起源古老且与基因活性有着复杂的联系，但进化允许基因组组织发生重大变化。
