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

Farr, Stephen E.; Woods, Esmae J.; Joseph, Jerelle A.; Garaizar, Adiran; Collepardo-Guevara, Rosana

doi:10.1101/2020.11.23.391599

Cited by 8 publications

(12 citation statements)

References 158 publications

(243 reference statements)

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“…We represented protein and DNA molecules with one coarsegrained bead per amino acid or nucleotide. Models of similar resolutions have been widely used to study IDPs [64][65][66][67][68] and protein-DNA complexes [69][70][71][72][73][74][75][76][77] with great success. The MOFF force field for proteins 39 and molecular renormalization group coarse-graining model (MRG-CG) for the DNA 40 were combined together to describe protein-DNA interactions under implicit solvation.…”

Section: Methodsmentioning

confidence: 99%

On the stability and layered organization of protein-DNA condensates

Latham

Zhang

2021

Preprint

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Multi-component phase separation is emerging as a key mechanism for the formation of biological condensates that play essential roles in signal sensing and transcriptional regulation. The molecular factors that dictate these condensates’ stability and spatial organization are not fully understood, and it remains challenging to predict their microstructures. Using a near-atomistic, chemically accurate force field, we studied the phase behavior of chromatin regulators that are crucial for heterochromatin organization and their interactions with DNA. Our computed phase diagrams recapitulated previous experimental findings on different proteins. They revealed a strong dependence of condensate stability on the protein-DNA mixing ratio as a result of balancing protein-protein interactions and charge neutralization. Notably, a layered organization was observed in condensates formed by mixing HP1, histone H1, and DNA. This layered organization may be of biological relevance as it enables cooperative DNA packaging between the two chromatin regulators: histone H1 softens the DNA to facilitate the compaction induced by HP1 droplets. Our study supports near atomistic models as a valuable tool for characterizing the structure and stability of biological condensates.

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Section: Methodsmentioning

confidence: 99%

On the stability and layered organization of protein-DNA condensates

Latham

Zhang

2021

Preprint

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“…6E, blue dash line). These increased peak values relative to those found for the spinodal condensates probably indicate that the higher compaction in spherical condensates further discourage intra-array n / n +2 stacking in favor of inter-array NCPs interactions, a conclusion supported by chromatin dynamics simulations (Farr et al, 2021). The second peak position (Fig.…”

Section: Resultsmentioning

confidence: 66%

Molecular Organization of the Early Stages of Nucleosome Phase Separation Visualized by Cryo-Electron Tomography

Zhang

Díaz-Celis

Onoa

et al. 2021

Preprint

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It has been proposed that the intrinsic property of nucleosome arrays to undergo liquid-liquid phase separation (LLPS) in vitro is responsible for chromatin domain organization in vivo. However, understanding nucleosomal LLPS has been hindered by the challenge to characterize the structure of resulting heterogeneous condensates. We used cryo-electron tomography and deep learning-based 3D reconstruction/segmentation to determine the molecular organization of condensates at various stages of LLPS. We show that nucleosomal LLPS involves a two-step process: a spinodal decomposition process yielding irregular condensates, followed by their unfavorable conversion into more compact, spherical nuclei that grow into larger spherical aggregates through accretion of spinodal material or by fusion with other spherical condensates. Histone H1 catalyzes more than 10-fold the spinodal-to-spherical conversion. We propose that this transition involves exposure of nucleosome hydrophobic surfaces resulting in modified inter-nucleosome interactions. These results suggest a physical mechanism by which chromatin may transition from interphase to metaphase structures.

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“…Work in drosophila suggests that H3K36me3 is enriched in gene bodies, in particular, in the region of transcribed genes distal to the transcription start site 53,54 . The increased proneness of H3K36me3 nucleosomes to partially unwrap suggests that H3K36me3 can directly affect higher order chromatin structure by increasing the heterogeneity of nucleosome-nucleosome contacts as well as the effective nucleosome valency 11 .…”

Section: Discussionmentioning

confidence: 99%

“…Post-translational modifications (PTMs) of histones play a key role in the formation of higher order chromatin structure 3,[9][10][11][12][13] , the recruitment of proteins and complexes with specific enzymatic activities 14 , and the maintenance of DNA repair 15 and replication 16 . Numerous histone variants and PTMs alter histone-histone and histone-DNA interactions [17][18][19] to yield nucleosomal structures with varying degrees of stability and DNA wrapping.…”

Section: Statement Of Significancementioning

confidence: 99%

Quantifying epigenetic modulation of nucleosome breathing by high-throughput AFM imaging

Konrad

Vanderlinden

Lipfert

2021

Preprint

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Nucleosomes are the basic units of chromatin and critical to the storage and expression of eukaryotic genomes. Chromatin accessibility and gene readout are heavily regulated by epigenetic marks of which post-translational modifications of histones play a key role. However, the mode of action and the structural implications on the single-molecule level of nucleosomes is often still poorly understood. Here, we apply a high-throughput AFM imaging and analysis pipeline to investigate the conformational landscape of the nucleosome variants H3K36me3, H3S10phos and H4K5/8/12/16ac. Our data set of >25,000 nucleosomes reveals nucleosomal unwrapping steps corresponding to 5 bp DNA. We find that H3K36me3 nucleosomes unwrap significantly more than wild type nucleosomes and additionally unwrap stochastically from both sides similar to CENP-A nucleosomes and in contrast to the highly anti-cooperative unwrapping of wild type nucleosomes. Nucleosomes with H3S10phos or H4K5/8/12/16ac modifications show unwrapping populations similar to wild type nucleosomes and also retain the same level of anti-cooperativity. Our findings help putting the mode of action of these modifications into context: While H3K36me3 likely partially acts by directly affecting nucleosome structure on the single-molecule level, H3S10phos and H4K5/8/12/16ac must predominantly act through higher-order processes. Our analysis pipeline is readily applicable to other nucleosome variants and will facilitate future high-resolution studies of the conformational landscape of nucleoprotein complexes.

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

Cited by 8 publications

References 158 publications

On the stability and layered organization of protein-DNA condensates

On the stability and layered organization of protein-DNA condensates

Molecular Organization of the Early Stages of Nucleosome Phase Separation Visualized by Cryo-Electron Tomography

Quantifying epigenetic modulation of nucleosome breathing by high-throughput AFM imaging

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