Near-atomic resolution nucleosome structures and their variations in interphase and metaphase chromosomes

HighlightsO_LI3.4~ [A] resolution nucleosome structures from interphase and metaphase chromosomes C_LIO_LINucleosome structures in chromosomes are more uniform than in free mono-nucleosomes C_LIO_LIHistone H1.8 binds to the nucleosome dyad axis in metaphase chromosomes C_LIO_LINucleosome structural variants are more prevalent in metaphase than in interphase C_LI SummaryStructural heterogeneity of nucleosomes in functional chromosomes is unknown. Here we report cryo-EM structures of nucleosomes isolated from interphase and metaphase chromosomes at up to 3.4 [A] resolution. Averaged chromosomal nucleosome structures are highly similar to canonical left-handed recombinant nucleosome crystal structures, with DNA being selectively stabilized at two defined locations. Compared to free mono-nucleosomes, which exhibit diverse linker DNA angles and large structural variations in H3 and H4, chromosomal nucleosome structures are much more uniform, characterized by a closed linker DNA angle with interactions between the H2A C-terminal tail and DNA. Exclusively for metaphase nucleosomes, structures of the linker histone H1.8 at the on-dyad position of nucleosomes can be reconstituted at 4.4 [A] resolution. We also report diverse minor nucleosome structural variants with rearranged core histone configurations, which are more prevalent in metaphase than in interphase chromosomes. This study presents structural characteristics of nucleosomes in interphase and mitotic chromosomes. NOTES TO READERSWe would like to emphasize the importance of supplemental movies S1-S3, which should greatly help readers to understand characteristics of the nucleosome structural variants that we report in this study.