Parasitic plasmids are anchored to inactive regions of eukaryotic chromosomes through a nucleosome signal [Hi-C]

Natural plasmids are common in prokaryotes, but few have been documented in eukaryotes. The natural 2µ plasmid present in the yeast Saccharomyces cerevisiae is one of these best-characterized exceptions. This highly stable genetic element has coexisted with its host for millions of years, faithfully segregating at each cell division through a mechanism that remains unclear. Using proximity ligation methods (such as Hi-C, Micro-C) to map the contacts between 2µ plasmid and yeast chromosomes under dozens of different biological conditions, we found that the plasmid is tethered preferentially to regions with low transcriptional activity, often corresponding to long, inactive genes. These contacts do not depend on common chromosome-structuring factors, such as members of the structural maintenance of chromosome complexes (SMC) but depend on a nucleosome-encoded signal associated with RNA Pol II depletion. They appear stable throughout the cell cycle and can be established within minutes. This chromosome hitchhiking strategy may extend beyond the 2µ plasmid/S. cerevisiae pair, as suggested by the binding pattern of the natural eukaryotic plasmid Ddp5 along silent chromosome regions of the amoeba Dictyostelium discoideum. Overall design: We explored the anchoring of parasitic plasmids with main chromosomes by performing Hi-C on various hosts and in different conditions for S.cerevisiae.

天然质粒在原核生物中广泛存在，但已被报道的真核生物天然质粒却极为稀少。存在于酿酒酵母（Saccharomyces cerevisiae）中的天然2µ质粒（2µ plasmid）便是这类得到最充分表征的例外之一。这一高度稳定的遗传元件已与其宿主共存数百万年，可在每次细胞分裂时精准完成分离，但其背后的具体调控机制仍未明确。我们借助邻近连接法（如Hi-C、Micro-C），在数十种不同生物学条件下绘制了2µ质粒与酵母染色体的互作图谱，发现该质粒优先锚定在转录活性较低的区域——这类区域通常对应长片段的非活性基因。这类互作并不依赖常见的染色体结构调控因子，如染色体结构维持复合物（SMC）成员，但却依赖一种由核小体编码、与RNA聚合酶II（RNA Pol II）耗竭相关的信号。该锚定模式在整个细胞周期中均保持稳定，且可在数分钟内完成建立。天然真核质粒Ddp5在盘基网柄菌（Dictyostelium discoideum）沉默染色体区域的结合模式提示，这种染色体“搭便车”策略可能并不局限于2µ质粒-酿酒酵母这一组合。实验整体设计：我们通过对酿酒酵母开展多宿主、多条件下的Hi-C实验，探究了寄生质粒与宿主主染色体的锚定机制。