Correlative visible light and soft X-ray tomography of in-situ mesoscale heterochromatin organization.

Recent evidence has revealed that cellular aging is accompanied by alterations in DNA methylation and histone modifications leading to a decrease in nucleosome packing density and heterochromatin remodeling. While these observations were obtained with multi-omics data (eg. Hi-C, ATAC-seq), the underlying ultrastructural mechanisms of mesoscale heterochromatin reorganization during cellular aging are still unclear. Towards this, we developed correlative light microscopy and cryo-soft X-ray tomography to analyze the alterations in heterochromatin organization in human mammary fibroblast cells. Our analysis revealed the micro-domain organization of heterochromatin structure with the mean domain size of 115 nm in the intact and hydrated state of cells. Upon addition of histone deacetylase inhibitor, that phenocopied aging, we observed a marked decrease in the heterochromatin density distribution, disruption of microdomains, and decrease in chromatin compaction length scales. To validate these observations, we also developed a bidisperse copolymer model in a confined volume using Brownian dynamics simulations. Collectively, our results provide direct evidence of mesoscale domains in heterochromatin packing and their alterations during cellular aging