巴塞罗那科技学院Arnau Sebé-Pedrós小组的一项最新研究报道了染色质环是动物调控基因组的祖先标志。该研究于2025年5月7日发表于国际一流学术期刊《自然》杂志上。

为了追踪动物基因组调控的进化起源，该团队将高分辨率染色体构象捕获与表观基因组标记和基因表达数据相结合，分析了非双侧动物（海绵动物、栉水母、扁藻和刺胞动物）及其最接近的单细胞近亲（鱼孢子动物、丝状动物和鞭虫动物）基因组的物理组织。他们的比较分析表明，染色质环是栉水母、扁藻和刺胞动物基因组结构的保守特征。这些序列决定的远端接触包括启动子-增强子和启动子-启动子相互作用。相比之下，在动物的单细胞近亲中没有染色质环。他们的发现表明，空间基因组调控在动物进化的早期就出现了。这种进化创新引入了调控复杂性，最终促进了动物发育程序和细胞类型库的多样化。

研究人员表示，在双边动物中，基因调控是由线性和空间调控信息的组合形成的。基因组上的调控元件通过染色质区隔化、邻近基因组区域的隔离和染色质环将远端顺式调控序列聚集在一起，被整合到基因调控景观中。然而，这些调控特征的进化是未知的，因为大多数动物谱系的三维基因组结构仍未被探索。

附：英文原文

Title: Chromatin loops are an ancestral hallmark of the animal regulatory genome

Author: Kim, Iana V., Navarrete, Cristina, Grau-Bov, Xavier, Iglesias, Marta, Elek, Anamaria, Zolotarov, Grygoriy, Bykov, Nikolai S., Montgomery, Sean A., Ksiezopolska, Ewa, Caas-Armenteros, Didac, Soto-Angel, Joan J., Leys, Sally P., Burkhardt, Pawel, Suga, Hiroshi, de Mendoza, Alex, Marti-Renom, Marc A., Seb-Pedrs, Arnau

Issue&Volume: 2025-05-07

Abstract: In bilaterian animals, gene regulation is shaped by a combination of linear and spatial regulatory information. Regulatory elements along the genome are integrated into gene regulatory landscapes through chromatin compartmentalization1,2, insulation of neighbouring genomic regions3,4 and chromatin looping that brings together distal cis-regulatory sequences5. However, the evolution of these regulatory features is unknown because the three-dimensional genome architecture of most animal lineages remains unexplored6,7. To trace the evolutionary origins of animal genome regulation, here we characterized the physical organization of the genome in non-bilaterian animals (sponges, ctenophores, placozoans and cnidarians)8,9 and their closest unicellular relatives (ichthyosporeans, filastereans and choanoflagellates)10 by combining high-resolution chromosome conformation capture11,12 with epigenomic marks and gene expression data. Our comparative analysis showed that chromatin looping is a conserved feature of genome architecture in ctenophores, placozoans and cnidarians. These sequence-determined distal contacts involve both promoter–enhancer and promoter–promoter interactions. By contrast, chromatin loops are absent in the unicellular relatives of animals. Our findings indicate that spatial genome regulation emerged early in animal evolution. This evolutionary innovation introduced regulatory complexity, ultimately facilitating the diversification of animal developmental programmes and cell type repertoires.

DOI: 10.1038/s41586-025-08960-w

Source: https://www.nature.com/articles/s41586-025-08960-w