Summary
Structural 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 Å 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 Å 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.
Highlights
3.4~ Å resolution nucleosome structures from interphase and metaphase chromosomes
Nucleosome structures in chromosomes are more uniform than in free mono-nucleosomes
Histone H1.8 binds to the nucleosome dyad axis in metaphase chromosomes
Nucleosome structural variants are more prevalent in metaphase than in interphase
NOTES TO READERS We 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.
Competing Interest Statement
H.F. is affiliated with Graduate School of Medical Sciences, Weill Cornell Medicine, and Cell Biology Program, the Sloan Kettering Institute. The authors declare that no competing financial interests exist.
Footnotes
In response to a comment to our bioRxiv preprint (BIORXIV/2020/380386, Near-atomic resolution nucleosome structures and their variations in interphase and metaphase chromosomes), we wonder if we could make a few minor changes to the title of our submitted paper. The new title is "Nucleosome structural variations in interphase and metaphase chromosomes." We would appreciate it if you could change the title of the web page of this paper to avoid confusion in the citations.