Compromised 2-start zigzag chromatin folding in immature mouse retina cells driven by irregularly spaced nucleosomes with short DNA linkers

The formation of condensed heterochromatin is critical for establishing
cell-specific transcriptional programs. To reveal structural transitions
underlying heterochromatin formation in maturing mouse rod photoreceptors,
we apply cryo-EM tomography, AI-assisted denoising, and molecular
modeling. We find that chromatin isolated from immature retina cells
contains many closely apposed nucleosomes with extremely short or absent
nucleosome linkers, which are inconsistent with the typical two-start
zigzag chromatin folding. In mature retina cells, the fraction of
short-linker nucleosomes is much lower, supporting stronger chromatin
compaction. By Cryo-EM-assisted nucleosome interaction capture, we observe
that chromatin in immature retina is enriched with i±1 interactions while
chromatin in mature retina contains predominantly i±2 interactions typical
of the two-start zigzag. By mesoscale modeling and computational
simulation, we clarify that the unusually short linkers typical of
immature retina are sufficient to inhibit the two-start zigzag and
chromatin compaction by the interference of very short linkers with linker
DNA stems. We propose that this short linker composition renders
nucleosome arrays more open in immature retina and that, as the linker DNA
length increases in mature retina, chromatin becomes globally condensed
via tight zigzag folding. This mechanism may be broadly utilized to
introduce higher chromatin folding entropy for epigenomic plasticity.