Histones and associated chromatin proteins have essential functions in eukaryotic genome organization and regulation. Despite this fundamental role in eukaryotic cell biology, we lack a phylogenetically comprehensive understanding of chromatin evolution. Here, we combine comparative proteomics and genomics analysis of chromatin in eukaryotes and archaea. Proteomics uncovers the existence of histone post-translational modifications in archaea. However, archaeal histone modifications are scarce, in contrast with the highly conserved and abundant marks we identify across eukaryotes. Phylogenetic analysis reveals that chromatin-associated catalytic functions (for example, methyltransferases) have pre-eukaryotic origins, whereas histone mark readers and chaperones are eukaryotic innovations. We show that further chromatin evolution is characterized by expansion of readers, including capture by transposable elements and viruses. Overall, our study infers detailed evolutionary history of eukaryotic chromatin: from its archaeal roots, through the emergence of nucleosome-based regulation in the eukaryotic ancestor, to the diversification of chromatin regulators and their hijacking by genomic parasites.

组蛋白和相关染色质蛋白在真核基因组组织和调控中具有重要作用。尽管在真核细胞生物学中具有这一基本作用，但我们缺乏对染色质进化的系统发育全面了解。在这里，我们结合了真核生物和古细菌染色质的比较蛋白质组学和基因组学分析。蛋白质组学揭示了古细菌中组蛋白翻译后修饰的存在。然而，与我们在真核生物中发现的高度保守和丰富的标记相比，古菌组蛋白修饰很少。系统发育分析表明，染色质相关的催化功能（例如，甲基转移酶）具有前真核起源，而组蛋白标记阅读器和伴侣是真核生物的创新。我们表明，进一步的染色质进化以阅读器的扩展为特征，包括被转座因子和病毒捕获。总体而言，我们的研究推断了真核染色质的详细进化历史：从其古菌根，到真核祖先中基于核小体的调控的出现，到染色质调控因子的多样化以及它们被基因组寄生虫劫持。