Mesoscale Modeling and Single-Nucleosome Tracking Reveal Remodeling of Clutch Folding and Dynamics in Stem Cell Differentiation

Abstract

Highlights d Mesoscale modeling of the Pou5f1 gene shows cell-typespecific nucleosome clutch patterns d H2B dynamics is cell-type specific and correlates with nucleosome clutch patterns d Linker histone H1 plays an important role in regulating H2B dynamics

In Diverse Conditions Intrinsic Chromatin Condensates Have Liquid-like Material Properties

“…Superresolution and single molecule fluorescence imaging studies have shown that nucleosomes compact into 30-50 nm clutches (Ricci et al, 2015), which further assemble into domains of ~100-300 nm in radius (Ashwin et al, 2019;Itoh et al, 2021;Lakadamyali and Cosma, 2020;Nozaki et al, 2017b;Otterstrom et al, 2019). Analyses of their motion has shown that individual nucleosomes move within these domains on tens of milliseconds timescales (Gómez-García et al, 2021;Lerner et al, 2020), and the domains themselves move on hundreds of milliseconds to seconds timescales (Ashwin et al, 2019;Hajjoul et al, 2013;Itoh et al, 2021;Levi et al, 2005;Marshall et al, 1997;Nozaki et al, 2017b). In both regimes, movement is subdiffusive and/or confined (Ashwin et al, 2019;Gómez-García et al, 2021;Hajjoul et al, 2013;Itoh et al, 2021;Levi et al, 2005;Marshall et al, 1997;Nozaki et al, 2017a), in part due to constraints on a given chromatin segment imparted by adhesions to surrounding structures, which increase with length of the segment (i.e.…”

“…Analyses of their motion has shown that individual nucleosomes move within these domains on tens of milliseconds timescales (Gómez-García et al, 2021;Lerner et al, 2020), and the domains themselves move on hundreds of milliseconds to seconds timescales (Ashwin et al, 2019;Hajjoul et al, 2013;Itoh et al, 2021;Levi et al, 2005;Marshall et al, 1997;Nozaki et al, 2017b). In both regimes, movement is subdiffusive and/or confined (Ashwin et al, 2019;Gómez-García et al, 2021;Hajjoul et al, 2013;Itoh et al, 2021;Levi et al, 2005;Marshall et al, 1997;Nozaki et al, 2017a), in part due to constraints on a given chromatin segment imparted by adhesions to surrounding structures, which increase with length of the segment (i.e. number of adhesions) (Chubb et al, 2002;Hajjoul et al, 2013).…”

“…Movement on these small scales is thought to primarily occur via passive thermal fluctuations rather than actively driven processes (Ashwin et al, 2019;Chubb et al, 2002;Hajjoul et al, 2013;Levi et al, 2005;Marshall et al, 1997;Nozaki et al, 2017b), although on longer timescales ATP-dependent jumps in position are also observed (Levi et al, 2005). Thus, short range/timescale movement reflect the dynamics of local internucleosome contacts that are subject to changes induced by histone acetylation and binding of linker histone H1 (Gómez-García et al, 2021;Otterstrom et al, 2019). These local dynamics are thought necessary for many genome functions, such as enhancer-promoter interactions (Chen et al, 2018), loop extrusion by SMC complexes (Davidson and Peters, 2021;Kim et al, 2019), and homologous pairing of sequences during meiosis and DNA repair (Hauer and Gasser, 2017;Kim et al, 2019).…”

Nucleosome plasticity is a critical element of chromatin liquid–liquid phase separation and multivalent nucleosome interactions

“…Nucleosomes within disordered chromatin are proposed to form heterogeneous groups of variable sizes and densities—interspersed with nucleosome-free regions 23 . Furthermore, the density of nucleosomes, rather than the structure of the 30-nm fiber, is what seems to distinguish different chromatin regions (e.g., nucleosome density is higher in heterochromatin than in euchromatin) 16 , 23 , and change upon differentiation 24 . Sequencing-based methods that can resolve chromatin interactions in situ at single-nucleosome resolution—i.e., micrococcal nuclease chromosome conformation assay (Micro-C) 25 , 26 , ionizing radiation-induced spatially correlated cleavage of DNA with sequencing (RICC-seq) 27 , and high-throughput chromosome conformation capture with nucleosome orientation (Hi-CO) 28 —suggest that the irregular organization of chromatin is underpinned by dominant interactions among i and i ± 2 nucleosomes.…”

“…Many of these parameters can independently enable chromatin polymorphism, triggering the folding of 10-nm fibers into irregular loops, hairpins, and bends 21 . Indeed, irregular nucleosome spacing 21 , 32 , nucleosome-free regions 23 , 24 , 32 – 34 , heterogeneous on/off dyad binding of linker histone proteins to the nucleosome 35 , 36 , low linker histone concentrations or subtype variations 36 , inhomogeneous distributions of post-translational modifications 37 , and the disordered nature of the linker histone protein 38 can independently give rise to a plethora of nucleosome orientations and interactions. In concert, these factors can further amplify or control chromatin polymorphism 34 , 37 , 39 .…”