Topo-seq reveals DNA topological memory of nucleosomes

Each nucleosome constrains a DNA linking number difference (∆Lk) of about -1.26, but whether this capacity to restrain negative DNA supercoils is uniform across the genome is unknown. Therefore, we determined the ∆Lk restrained by 4000 individual nucleosomes in yeast cells. To do this, we placed each nucleosome in a circular minichromosome and conducted Topo-seq, a novel high-throughput procedure to inspect the topology of multiple DNA molecules in a single gel electrophoresis. We found that nucleosomes inherently restrain distinct ∆Lk values depending on their genomic origin.每个核小体（nucleosome）可约束约-1.26的DNA连接数差值（DNA linking number difference，ΔLk），但这种约束负DNA超螺旋的能力在全基因组范围内是否均一尚不明确。为此，我们测定了酵母细胞中4000个独立核小体所约束的ΔLk值。实验中，我们将每个核小体置于环状微型染色体（circular minichromosome）内，并开展了拓扑测序（Topo-seq）——一种可在单次凝胶电泳中同时检测多个DNA分子拓扑结构的新型高通量技术。研究发现，核小体所约束的ΔLk值本就存在差异，且该差异取决于其基因组来源。