Tetranucleosome Interactions Drive Chromatin Folding

Abstract

The multiscale organizational structure of chromatin in eukaryotic cells is instrumental to DNA transcription, replication, and repair. At mesoscopic length scales, nucleosomes pack in a manner that serves to regulate gene expression through condensation and expansion of the genome. The particular structures that arise and their respective thermodynamic stabilities, however, have yet to be fully resolved. In this study, we combine molecular modeling using the 1CPN mesoscale model of chromatin with nonlinear manifold learning to identify and characterize the structure and free energy of metastable states of short chromatin segments comprising between 4- and 16-nucleosomes. Our results reveal the formation of two previously characterized tetranucleosomal conformations, the “α-tetrahedron” and the “β-rhombus”, which have been suggested to play an important role in the accessibility of DNA and, respectively, induce local chromatin compaction or elongation. The spontaneous formation of these motifs is potentially responsible for the slow nucleosome dynamics observed in experimental studies. Increases of the nucleosome repeat length are accompanied by more pronounced structural irregularity and flexibility and, ultimately, a dynamic liquid-like behavior that allows for frequent structural reorganization. Our findings indicate that tetranucleosome motifs are intrinsically stable structural states, driven by local internucleosomal interactions, and support a mechanistic picture of chromatin packing, dynamics, and accessibility that is strongly influenced by emergent local mesoscale structure.

Robustness of trinucleosome compaction to A-tract mediated linker histone orientation

“…While building the models, apart from the single spFRET restraint, we also ensured that the L-DNAs were not kinked or bent at an angle. Thus, as the inner L-DNAs are straight, Nuc 1 and 3 stack on top of each other (Figure 3), resembling the canonical two-start helical arrangement [46] as predicted and observed for 187 NRL nucleosomes [47][48][49]. The stacking is optimal as confirmed by aligning the modelled structure (for A-near and A-far) to the structures 6HKT [48] and 6L49 [50].…”

Chromatin fiber breaks into clutches under tension and crowding

“…Nucleosome clutch formation is not specific to a particular end-to-end distance and can be readily seen in structures with smaller distances as well (Figure 4 and Supplementary Figure S12 ). We note that the nucleosomes that remain in contact are not perfectly stacked as in the crystal structure of a tetranucleosome ( 68 ), but are somewhat irregular as configurations observed in prior simulations ( 49 , 63 ) and in vivo experiments ( 19 , 74–76 ). Further stretching the chromatin eventually leads to configurations with most of the outer nucleosomal DNA unwrapped.…”

Emerging Contributions of Solid-State NMR Spectroscopy to Chromatin Structural Biology

“…Mononucleosome sediments with low levels of Mg 2+ lacked the long-range order expected for stacked fibers formed by high Mg 2+ concentrations ( le Paige et al, 2021 ). Such irregular packing may illuminate the transient nucleosome-nucleosome interactions that dominate when nucleosomes are not restricted into ordered arrays ( Bilokapic et al, 2018 ; Sanulli et al, 2019 ; Alvarado et al, 2021 ). Thus, samples prepared by sedimentation and low Mg 2+ concentrations may prove crucial for resolving the transient interactions that lead to chromatin compaction and regulation ( Gibson et al, 2019 ; Khanna et al, 2019 ; Sanulli et al, 2019 ; Kantidze and Razin, 2020 ).…”

“…Building upon these studies, the interactions of many adjacent nucleosomes can be addressed. The chromatin context is important for biomolecular recognition; some chromatin modulator complexes are much larger than a nucleosome and can sense nearby nucleosomes ( Yang et al, 2006 ; He et al, 2020 ), many architectural proteins are multivalent and can simultaneously interact with several nucleosomes ( Machida et al, 2018 ; Poepsel et al, 2018 ), and neighboring nucleosomes can stack atop each other, thereby competing with chromatin modulators for binding sites ( Bilokapic et al, 2018 ; Sanulli et al, 2019 ; Alvarado et al, 2021 ). The fiber context is also necessary for packaging, as nucleosomes are strung together and densities get closer to those observed in cells (10–100 mg/ml) ( Imai et al, 2017 ; Hancock, 2018 ; Kim and Guck, 2020 ), chromatin can undergo phase separation into a highly viscous solid-like material ( Strickfaden et al, 2020 ).…”