# Direct visualization and tracing of chromatin folding in the Drosophila embryo

## TL;DR

This study uses cryo-electron tomography to directly visualize how chromatin folds in Drosophila embryos, revealing an irregular zig-zag pattern and diverse nucleosome conformations.

## Contribution

The study provides the first direct in situ visualization of chromatin folding and nucleosome conformations in a living organism using cryo-electron tomography.

## Key findings

- Chromatin folds in an irregular zig-zag pattern with low linker DNA bending.
- Nucleosomes show conformational variability, including open, closed, and gaping states.
- Non-octameric nucleosome-like particles with one or three DNA gyres were observed.

## Abstract

Chromatin organization, through the assembly of DNA with histones and the folding of nucleosome chains, regulates DNA accessibility for transcription, DNA replication and repair. Although models derived from in vitro studies have proposed distinct nucleosome chain geometries, the organization of chromatin within the crowded cell nucleus remains elusive. Using cryo-electron tomography of thin vitreous sections, we directly observed the path of nucleosomal and linker DNA in situ from a flash-frozen organism - Drosophila embryos. We quantified linker length and curvature, characterizing an irregular zig-zag chromatin-folding motif, with a low degree of linker bending. Nucleosome conformations could be identified on individual particles in favorable orientations without structure averaging. Additionally, we observed particles that accommodate a number of DNA gyres ranging from less than one to up to three, which resemble previously proposed non-octameric nucleosomal particles with variable DNA wrapping.

DNA is organized in quasiperiodic arrays of nucleosomes connected by a DNA linker, but how these arrays fold in cell remains unclear. This study uses cryo-electron tomography of Drosophila embryos to directly visualize linker DNA, revealing an irregular zig-zag chromatin fold.

Cryo-ET visualizes chromatin in its native cellular and organismal context.Individual DNA linkers were traced between nucleosomes enabling direct measurement of their length and curvature.An irregular zig-zag chromatin geometry was revealed upon tracing nucleosome arrays.Nucleosomes exhibit rich conformational variability, including open, closed, and gaping states.Nucleosome-like particles containing one or three DNA gyres were observed, consistent with the presence of tetrasomes, hemisomes, and overlapping dinucleosomes in situ.

Cryo-ET visualizes chromatin in its native cellular and organismal context.

Individual DNA linkers were traced between nucleosomes enabling direct measurement of their length and curvature.

An irregular zig-zag chromatin geometry was revealed upon tracing nucleosome arrays.

Nucleosomes exhibit rich conformational variability, including open, closed, and gaping states.

Nucleosome-like particles containing one or three DNA gyres were observed, consistent with the presence of tetrasomes, hemisomes, and overlapping dinucleosomes in situ.

Cryo-electron tomography allows the direct observation of linker DNA geometry and nucleosome conformational variability in a near-native cellular context.