A simulation model of heterochromatin formation at submolecular detail

Williams, Michael R.; Yan, Xiaokang; Hathaway, Nathaniel A.; Kireev, Dmitri

doi:10.1016/j.isci.2022.104590

Cited by 4 publications

(10 citation statements)

References 92 publications

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“…To gain a mechanistic insight at molecular resolution into H3K9me3 propagation in control lines (CT) and SETDB1 knockdown cells, we made use of our previously described Monte Carlo simulation model ( 33 ). The simulated system included a chromatin fiber approximately matching the size of the Oct4 promoter region (20 kb), HP1, the three known H3K9 methyltransferases (G9a, SETDB1, and SUV39H), and a generic demethylase.…”

Section: Resultsmentioning

confidence: 99%

“…The simulated system consists of an unmethylated chromatin fiber (102 nucleosomes) and 102 copies of each protein—HP1, G9a, SUV39H, SETDB1, and a generic lysine demethylase (KDM)—corresponding to a putative cellular concentration level [on the order of 10 µM ( 71 )]. The particle-based chromatin model, the Monte Carlo simulation method, and all simulation settings (box, voxels, time step, and output) were used as previously described ( 33 ). The time step of 1 μs was chosen to maximize the sampling rate while keeping the particle displacements within the system's resolution, that is, by avoiding overstretching the particle-to-particle tethers.…”

Section: Methodsmentioning

confidence: 99%

“…The protein–protein interactions for the four enzymes include binding of the bind particle of each HMT to HP1 and binding of KDM to methylated H3K9. The interactions in the simulated system occur as previously described ( 33 ) and are governed by the association ( p a ) and dissociation ( p d ) probabilities that parameterize stochastic processes “carried” by the interacting particles (see Tables S4 and S5 for a full list of interaction parameters). The p a and p d parameters were inferred from experimental data based on the current knowledge of how the three HMTs bind to chromatin.…”

Section: Methodsmentioning

confidence: 99%

“…Previous work has demonstrated that SETDB1 disruption can lead to the gene upregulation and changes in the chromatin state; however, we do not know how SETDB1 disruption led to a failure of heterochromatin formation or gene regulation. In our previous work, we have combined biological and computational simulation experiments to understand the HP1α-induced heterochromatin formation process ( 33 ). This work extends our previous work to probe the contribution of SETDB1 in HP1α-induced heterochromatin formation using both experimental and computational methods.…”

Section: Introductionmentioning

confidence: 99%

“…Previously, computational simulations proved successful in modeling various aspects of the chromatin structural transformations ( 55–64 ), although most of the reported models were tuned to simulate mega-base systems ( 55 , 58–60 , 65 ). Recently, we introduced a Monte Carlo particle-based model to a submolecular detail in order to more accurately reflect the entropic burden affecting the dynamics of heterochromatin formation ( 33 ). Despite neglecting important aspects of the system's energetics, the model was able to provide a comprehensive spatial and temporal characterization of the heterochromatin formation process suggesting that heterochromatin formation is a largely entropy-driven process.…”

Section: Introductionmentioning

confidence: 99%

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Relationship between lysine methyltransferase levels and heterochromatin gene repression in living cells and in silico

et al. 2023

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Gene regulation plays essential roles in all multicellular organisms allowing for different specialized tissue types to be generated from a complex genome. Heterochromatin-driven gene repression, associated with a physical compaction of the genome, is a pathway involving core components that are conserved from yeast to human. Posttranslational modification of chromatin is a critical component of gene regulation. Specifically, trimethylation of the nucleosome component Histone 3 at lysine 9 (H3K9me3) is a key feature of this pathway along with the hallmark heterochromatin protein 1 (HP1). Histone methyltransferases are recruited by HP1 to deposit H3K9me3 marks which nucleate and recruit more HP1 in a process that spreads from the targeting site to signal for gene repression. One of the enzymes recruited is SETDB1, a methyltransferase which putatively catalyzes posttranslational methylation marks on H3K9. To better understand the contribution of SETDB1 in heterochromatin formation, we downregulated SETDB1 through knock down by a dCas9-KRAB system and examined heterochromatin formation in a chromatin in vivo assay (CiA-Oct4). We studied the contribution of SETDB1 to heterochromatin formation kinetics in a developmentally crucial locus, Oct4. Our data demonstrate that SETDB1 reduction led to a delay in both gene silencing and in H3K9me3 accumulation. Importantly, SETDB1 knock-down to a ∼50% level did not stop heterochromatin formation completely. Particle-based Monte-Carlo simulations in three-dimensional space with explicit representation of key molecular processes enabled the elucidation of how SETDB1 downregulation affects the individual molecular processes underlying heterochromatin formation.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Relationship between lysine methyltransferase levels and heterochromatin gene repression in living cells and in silico

et al. 2023

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HP1-driven phase separation recapitulates the thermodynamics and kinetics of heterochromatin condensate formation

Tortora

Brennan

Karpen

et al. 2023

Proc. Natl. Acad. Sci. U.S.A.

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The spatial segregation of pericentromeric heterochromatin (PCH) into distinct, membrane-less nuclear compartments involves the binding of Heterochromatin Protein 1 (HP1) to H3K9me2/3-rich genomic regions. While HP1 exhibits liquid–liquid phase separation properties in vitro, its mechanistic impact on the structure and dynamics of PCH condensate formation in vivo remains largely unresolved. Here, using a minimal theoretical framework, we systematically investigate the mutual coupling between self-interacting HP1-like molecules and the chromatin polymer. We reveal that the specific affinity of HP1 for H3K9me2/3 loci facilitates coacervation in nucleo and promotes the formation of stable PCH condensates at HP1 levels far below the concentration required to observe phase separation in purified protein assays in vitro. These heterotypic HP1–chromatin interactions give rise to a strong dependence of the nucleoplasmic HP1 density on HP1-H3K9me2/3 stoichiometry, consistent with the thermodynamics of multicomponent phase separation. The dynamical cross talk between HP1 and the viscoelastic chromatin scaffold also leads to anomalously slow equilibration kinetics, which strongly depend on the genomic distribution of H3K9me2/3 domains and result in the coexistence of multiple long-lived, microphase-separated PCH compartments. The morphology of these complex coacervates is further found to be governed by the dynamic establishment of the underlying H3K9me2/3 landscape, which may drive their increasingly abnormal, aspherical shapes during cell development. These findings compare favorably to 4D microscopy measurements of HP1 condensate formation in live Drosophila embryos and suggest a general quantitative model of PCH formation based on the interplay between HP1-based phase separation and chromatin polymer mechanics.

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Two-way feedback between chromatin compaction and histone modification state explains Saccharomyces cerevisiae heterochromatin bistability

Movilla Miangolarra,

Saxton,

Yan

et al. 2024

Proc. Natl. Acad. Sci. U.S.A.

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Compact chromatin is closely linked with gene silencing in part by sterically masking access to promoters, inhibiting transcription factor binding and preventing polymerase from efficiently transcribing a gene. However, a broader hypothesis suggests that chromatin compaction can be both a cause and a consequence of the locus histone modification state, with a tight bidirectional interaction underpinning bistable transcriptional states. To rigorously test this hypothesis, we developed a mathematical model for the dynamics of the HMR locus in Saccharomyces cerevisiae , that incorporates activating histone modifications, silencing proteins, and a dynamic, acetylation-dependent, three-dimensional locus size. Chromatin compaction enhances silencer protein binding, which in turn feeds back to remove activating histone modifications, leading to further compaction. The bistable output of the model was in good agreement with prior quantitative data, including switching rates from expressed to silent states (and vice versa), and protein binding/histone modification levels within the locus. We then tested the model by predicting changes in switching rates as the genetic length of the locus was increased, which were then experimentally verified. Such bidirectional feedback between chromatin compaction and the histone modification state may be a widespread and important regulatory mechanism given the hallmarks of many heterochromatic regions: physical chromatin compaction and dimerizing (or multivalent) silencing proteins.

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A simulation model of heterochromatin formation at submolecular detail

Cited by 4 publications

References 92 publications

Relationship between lysine methyltransferase levels and heterochromatin gene repression in living cells and in silico

Relationship between lysine methyltransferase levels and heterochromatin gene repression in living cells and in silico

HP1-driven phase separation recapitulates the thermodynamics and kinetics of heterochromatin condensate formation

Two-way feedback between chromatin compaction and histone modification state explains Saccharomyces cerevisiae heterochromatin bistability

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