Molecular interactions underlying the phase separation of HP1α: role of phosphorylation, ligand and nucleic acid binding

Her, Cheenou; Phan, Tien M.; Jovic, Nina; Kapoor, Utkarsh; Ackermann, Bryce E.; Rizuan, Azamat; Kim, Young C.; Mittal, Jeetain; Debelouchina, Galia T.

doi:10.1093/nar/gkac1194

Cited by 25 publications

(78 citation statements)

References 88 publications

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“…To understand this behavior and examine the interactions between HP1α and the nucleosome, we quantified the HP1α-DNA interactions by computing the intermolecular contact maps. Figure b shows that HP1α interacts with DNA through patches of positively charged lysine/arginine-rich regions in the hinge, NTE, and CD region, which is consistent with previous experimental and computational studies. ,,, Interestingly, we observed that while the HP1α form contacts with the entire DNA strand, the contact probabilities are generally higher for SHL near the dyad and at the DNA entry and exit sites, contrary to the SHL locations for histone core–DNA contacts (see SI Figure S7a). This suggests that histone tails, which interact favorably with DNA, compete with, and potentially antagonize the contacts between HP1α and DNA, thereby affecting the ability of DNA to promote LLPS of HP1α.…”

Section: Introductionsupporting

confidence: 90%

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Coarse-Grained Models to Study Protein–DNA Interactions and Liquid–Liquid Phase Separation

Kapoor,

Kim,

Mittal

2023

J. Chem. Theory Comput.

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Recent advances in coarse-grained (CG) computational models for DNA have enabled molecular-level insights into the behavior of DNA in complex multiscale systems. However, most existing CG DNA models are not compatible with CG protein models, limiting their applications for emerging topics such as protein− nucleic acid assemblies. Here, we present a new computationally efficient CG DNA model. We first use experimental data to establish the model's ability to predict various aspects of DNA behavior, including melting thermodynamics and relevant local structural properties such as the major and minor grooves. We then employ an all-atom hydropathy scale to define nonbonded interactions between protein and DNA sites, to make our DNA model compatible with an existing CG protein model (HPS-Urry), which is extensively used to study protein phase separation, and show that our new model reasonably reproduces the experimental binding affinity for a prototypical protein−DNA system. To further demonstrate the capabilities of this new model, we simulate a full nucleosome with and without histone tails, on a microsecond time scale, generating conformational ensembles and provide molecular insights into the role of histone tails in influencing the liquid−liquid phase separation (LLPS) of HP1α proteins. We find that histone tails interact favorably with DNA, influencing the conformational ensemble of the DNA and antagonizing the contacts between HP1α and DNA, thus affecting the ability of DNA to promote LLPS of HP1α. These findings shed light on the complex molecular framework that fine-tunes the phase transition properties of heterochromatin proteins and contributes to heterochromatin regulation and function. Overall, the CG DNA model presented here is suitable to facilitate micrometer-scale studies with sub-nm resolution in many biological and engineering applications and can be used to investigate protein−DNA complexes, such as nucleosomes, or LLPS of proteins with DNA, enabling a mechanistic understanding of how molecular information may be propagated at the genome level.

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Section: Introductionsupporting

confidence: 90%

“…Next, to perform phase coexistence simulation, we resize this cubic box and create an initial slab configuration of dimensions 17 × 17 × 100 nm 3 . After this initialization stage, we run the simulation for 5 μs at T = 320 K and 100 mM salt concentration, as was done in our previous study …”

Section: Introductionmentioning

confidence: 99%

Coarse-Grained Models to Study Protein–DNA Interactions and Liquid–Liquid Phase Separation

Kapoor,

Kim,

Mittal

2023

J. Chem. Theory Comput.

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“… 213 HP1α can form condensates, which has a regulatory effect on the growth of breast cancer. 49 , 215 The condensates of RBP non‐POU domain‐containing octamer binding (NONO) regulate tumor cell proliferation by binding to mRNA of proliferation‐related genes. 218 Mutations of speckle‐type pox virus and zinc finger protein alter the formation of condensates and promote breast cancer progression.…”

Section: Biomolecular Condensates Serve As Therapeutic Targets For Di...mentioning

confidence: 99%

“…AKAP95, a nuclear protein that regulates transcription and RNA splicing, supports tumorigenesis by forming condensates and regulating gene expression 213 . HP1α can form condensates, which has a regulatory effect on the growth of breast cancer 49,215 . The condensates of RBP non‐POU domain‐containing octamer binding (NONO) regulate tumor cell proliferation by binding to mRNA of proliferation‐related genes 218 .…”

Section: Biomolecular Condensates Serve As Therapeutic Targets For Di...mentioning

confidence: 99%

Biomolecular condensates: Formation mechanisms, biological functions, and therapeutic targets

Niu

Zhang

et al. 2023

MedComm

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Biomolecular condensates are cellular structures composed of membraneless assemblies comprising proteins or nucleic acids. The formation of these condensates requires components to change from a state of solubility separation from the surrounding environment by undergoing phase transition and condensation. Over the past decade, it has become widely appreciated that biomolecular condensates are ubiquitous in eukaryotic cells and play a vital role in physiological and pathological processes. These condensates may provide promising targets for the clinic research. Recently, a series of pathological and physiological processes have been found associated with the dysfunction of condensates, and a range of targets and methods have been demonstrated to modulate the formation of these condensates. A more extensive description of biomolecular condensates is urgently needed for the development of novel therapies. In this review, we summarized the current understanding of biomolecular condensates and the molecular mechanisms of their formation. Moreover, we reviewed the functions of condensates and therapeutic targets for diseases. We further highlighted the available regulatory targets and methods, discussed the significance and challenges of targeting these condensates. Reviewing the latest developments in biomolecular condensate research could be essential in translating our current knowledge on the use of condensates for clinical therapeutic strategies.

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“…Using these spectroscopic tools, we dissect the interactions of the CD domain and the CSD dimer with the nucleosome and capture the effect of HP1α phase separation on the nucleosome core and tails. We focus on the interactions between nucleosomes and HP1α phosphorylated at its NTE as this post-translational modification is constitutively present in cells and is a major driving force for phase separation in vitro . ,,, Our results indicate that phosphorylated HP1α primarily contacts the nucleosome through a CD–H3 K9me3 interaction without major rearrangements of the nucleosome core.…”

Section: Introductionmentioning

confidence: 99%

Phosphorylated HP1α–Nucleosome Interactions in Phase Separated Environments

Elathram,

Ackermann,

Clark

et al. 2023

J. Am. Chem. Soc.

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In the nucleus, transcriptionally silent genes are sequestered into heterochromatin compartments comprising nucleosomes decorated with histone H3 Lys9 trimethylation and a protein called HP1α. This protein can form liquid−liquid droplets in vitro and potentially organize heterochromatin through a phase separation mechanism that is promoted by phosphorylation. Elucidating the molecular interactions that drive HP1α phase separation and its consequences on nucleosome structure and dynamics has been challenging due to the viscous and heterogeneous nature of such assemblies. Here, we tackle this problem by a combination of solution and solid-state NMR spectroscopy, which allows us to dissect the interactions of phosphorylated HP1α with nucleosomes in the context of phase separation. Our experiments indicate that phosphorylated human HP1α does not cause any major rearrangements to the nucleosome core, in contrast to the yeast homologue Swi6. Instead, HP1α interacts specifically with the methylated H3 tails and slows the dynamics of the H4 tails. Our results shed light on how phosphorylated HP1α proteins may regulate the heterochromatin landscape, while our approach provides an atomic resolution view of a heterogeneous and dynamic biological system regulated by a complex network of interactions and post-translational modifications.

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Molecular interactions underlying the phase separation of HP1α: role of phosphorylation, ligand and nucleic acid binding

Cited by 25 publications

References 88 publications

Coarse-Grained Models to Study Protein–DNA Interactions and Liquid–Liquid Phase Separation

Coarse-Grained Models to Study Protein–DNA Interactions and Liquid–Liquid Phase Separation

Biomolecular condensates: Formation mechanisms, biological functions, and therapeutic targets

Phosphorylated HP1α–Nucleosome Interactions in Phase Separated Environments

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