Sequence-dependent activity and compartmentalization of foreign DNA in a eukaryotic nucleus [Hi-C]

In eukaryotes, DNA-associated protein complexes co-evolve with genomic sequence to orchestrate chromatin folding into functional chromosomes. Here, we investigate the relationship between DNA sequence and the spontaneous loading and activity of chromatin components in the absence of co-evolutions. Using bacterial genomes integrated into S. cerevisiae, which diverged from yeast up to 1.5 billion years ago, we show that nucleosomes, cohesins and the transcriptional machinery can lead to the formation of two different chromatin archetypes, one being transcribed and the other silent. These two archetypes also form on eukaryotic exogenous sequences, and depend on sequence composition. They do not mix in the nucleus, leading to a bipartite nuclear compartmentalisation reminiscent of the organization of vertebrate nuclei. Our findings represent a significant advance in understanding the primary molecular mechanisms that govern the co-option or silencing of DNA sequences integrated into foreign genomes during natural horizontal gene transfers, or in synthetic genomics projects. Overall design: We explored the spatial folding of bacterial chromosomes integrated in a eukaryotic environment by performing Hi-C of yeast strains containing linearized and telomerized bacterial chromosomes.

在真核生物中，DNA结合蛋白复合物（DNA-associated protein complexes）会与基因组序列协同进化，协同调控染色质折叠为功能性染色体。本研究旨在探究无协同进化条件下，DNA序列与染色质组分自发加载及活性之间的关联。我们采用整合至酿酒酵母（Saccharomyces cerevisiae，即S. cerevisiae）的细菌基因组开展实验——该酵母的演化分化时间可追溯至15亿年前——结果显示，核小体、黏连蛋白及转录机器可介导两种不同的染色质原型的形成，其一为转录活跃型，另一为转录沉默型。这两种染色质原型同样可在真核外源性序列上形成，且其形成依赖于序列的碱基组成特征。二者在细胞核内互不混合，形成双向分隔的核区室结构，这一组织模式与脊椎动物细胞核的染色质布局高度相似。本研究结果为理解自然水平基因转移或合成基因组学项目中，整合至异源基因组的DNA序列的招募或沉默的核心分子机制提供了重要进展。实验设计：本研究通过对携带线性化并端粒化细菌染色体的酵母菌株开展高通量染色体构象捕获（Hi-C）实验，探究了整合于真核环境中的细菌染色体的空间折叠模式。