SUMMARY
At the onset of mitosis, chromosomes condense into discrete bodies. This transformation involves rearrangement at the nucleosome level and has consequences for transcription, but the details remain unclear. Here, we use cryo-electron tomography to determine the 3-D arrangement of nucleosomes and other large nuclear features in interphase and mitotic fission yeast cells. Nucleosomes can form heterogenous clusters in both interphase and mitotic cells, but none the size of a Hi-C domain. Furthermore, the nucleosomes are mingled with two features: nucleosome-free pockets and ribosome-sized “megacomplexes”. Compared to interphase chromatin, the nucleosomes in mitotic chromatin pack in larger clusters. Furthermore, mitotic chromatin contained fewer megacomplexes. However, nearest-neighbor distance analysis revealed that mitotic nucleosome clusters have the same packing density as in interphase. Therefore, the uneven chromosome condensation helps explain a longstanding enigma of mitosis: most genes are silenced but a subset is upregulated.