Direct visualization and tracing of DNA fold in Drosophila embryo

ABSTRACT The chromatin machinery, with DNA-histone assembly and further folding of nucleosome chains, influences DNA availability for functional interactions necessary to the regulation of transcription, DNA replication and repair. Despite models based on in vitro studies, the nucleosome chain geometry 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 in intact flash-frozen organism - Drosophila embryo. We quantified linker length and curvature characterizing an irregular zig-zag chromatin folding motif, with a low degree of linker bending. Additionally, nucleosome conformational variability with non-canonical structures and non-octameric particles were observed as individual objects, without structure averaging, highlighting the high structural heterogeneity of native chromatin.