One fundamental yet elusive aspect of chromosome architecture is the topolome, which refers to how chromatin elements shape the path of DNA. Nucleosomes stabilise negative DNA supercoils, with most nucleosomes typically restraining a DNA linking number difference (∆Lk) of about -1.26. However, whether this capacity is uniform across the genome is unknown. Here, we calculated the ∆Lk restrained by over 4000 nucleosomes in yeast cells. To achieve this, we placed each nucleosome in a circular minichromosome and performed Topo-seq, a novel high-throughput procedure to inspect the topology of circular DNA libraries in a single gel electrophoresis. We discovered that nucleosomes inherently restrain distinct ∆Lk values depending on their genomic origin. Nucleosome DNA topologies differ significantly at gene bodies (∆Lk=-1.29), intergenic regions (∆Lk=-1.23), rDNA genes (∆Lk=-1.24) and telomeric regions (∆Lk=-1.07). Nucleosomes nearby the transcription start and termination sites also exhibit singular ∆Lk values. Our findings demonstrate that nucleosome DNA topology is imprinted by its native chromatin context and persists when the nucleosome is relocated. Therefore, the intrinsic topology of nucleosomal DNA emerges as a new determinant of chromatin architecture and function. Our findings also validate the potential of Topo-seq, laying the foundation for the field of topolomics.