Condensed chromatin behaves like a solid on the mesoscale in vitro and in living cells

Abstract

The association of nuclear DNA with histones to form chromatin is essential to the temporal and spatial control of eukaryotic genomes. In this study, we examined the physical state of chromatin in vitro and in vivo. Our in vitro studies demonstrate that MgCl2-dependent self-association of native chromatin fragments or reconstituted nucleosomal arrays produced supramolecular condensates whose constituents are physically constrained and solid-like. Liquid chromatin condensates could be generated in vitro, but only using non-physiological conditions. By measuring DNA mobility within heterochromatin and euchromatin in living cells, we show that chromatin also exhibits solid-like behavior in vivo. Representative heterochromatin proteins, however, displayed liquid-like behavior and coalesced around a solid chromatin scaffold. Remarkably, both euchromatin and heterochromatin showed solid-like behavior even when transmission electron microscopy revealed limited interactions between chromatin fibers. Our results therefore argue that chromatin is not liquid but exists in a solid-like material state whose properties are tuned by fiber-fiber interactions. INTRODUCTION:

Single-cell ATAC and RNA sequencing reveal pre-existing and persistent subpopulations of cells associated with relapse of prostate cancer

“…According to this analysis, specific subpopulations of PC cells are more subjected than others to TFs activity reprogramming. This is consistent with recent studies showing simultaneous detection of multiple transcription factors on single DNA molecules and TFs co-occupancy frequently occurring at sites of competition with nucleosomes (Strickfaden et al, 2020).…”

“…Along with others, we previously reported that AR overexpression is associated with chromatin reprogramming (Braadland et al, 2019; Jia et al, 2006; Tewari et al, 2012; Urbanucci et al, 2017). As transcriptionally permissive chromatin in open conformation is the first layer of gene regulation (Sönmezer et al, 2020; Strickfaden et al, 2020), we hypothesized that chromatin structure would be reshaped in ENZ-resistant cells and lead to modification of the transcriptome.…”

“…Non-genetic effects linked to epigenetics in PC drug resistance are even less understood. Chromatin structure and DNA accessibility to transcription factor (TF) DNA binding motifs is the first layer of gene regulation (Sönmezer et al, 2020; Strickfaden et al, 2020). For example, expression and activity of the Glucocorticoid Receptor and the pluripotent stem cell transcription factor Sox2 have been shown to promote enzalutamide (ENZ) resistance (Crona and Whang, 2017; Isikbay et al, 2014; Li et al, 2017a; Mu et al, 2017).…”

Phase separation by the polyhomeotic sterile alpha motif compartmentalizes Polycomb Group proteins and enhances their activity

“…53 ). Experiments with 12-nucleosome linear arrays (more than 4× smaller than the templates used here) indicate that while chromatin alone can form a liquid-like state that shows (slow) recovery in FRAP experiments 31 , in most conditions, chromatin forms condensates that behave as solids and do not recover in FRAP experiments, similar to chromatin in vivo 54 .…”

Heterogeneous interactions and polymer entropy decide organization and dynamics of chromatin domains

“…Whether chromatin is liquid-like, solid-like or gel-like has been a matter of intense discussion in the recent literature [10, 24, 48, 49]. In the phase separation picture, chromatin segments are thought to be “liquid-like”, dynamically exploring various configurations.…”