Entropy gives rise to topologically associating domains

Vasquez, Paula A.; Hult, Caitlin; Adalsteinsson, David; Lawrimore, Josh; Forest, M. Gregory; Bloom, Kerry

doi:10.1093/nar/gkw510

Cited by 40 publications

(42 citation statements)

References 80 publications

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“…2a, b). Thus, loss of circularity is accompanied by a significant increase in the HP1a immobile fraction, which we speculate is a result of more HP1a associating with the chromatin polymer, whose inherent elasticity introduces shape constraints 15 .…”

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confidence: 87%

Phase separation drives heterochromatin domain formation

Strom

Emelyanov

Mir

et al. 2017

Nature

1,525

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Constitutive heterochromatin is an important component of eukaryotic genomes that has essential roles in nuclear architecture, DNA repair and genome stability1, and silencing of transposon and gene expression2. Heterochromatin is highly enriched for repetitive sequences, and is defined epigenetically by methylation of histone H3 at lysine 9 and recruitment of its binding partner heterochromatin protein 1 (HP1). A prevalent view of heterochromatic silencing is that these and associated factors lead to chromatin compaction, resulting in steric exclusion of regulatory proteins such as RNA polymerase from the underlying DNA3. However, compaction alone does not account for the formation of distinct, multi-chromosomal, membrane-less heterochromatin domains within the nucleus, fast diffusion of proteins inside the domain, and other dynamic features of heterochromatin. Here we present data that support an alternative hypothesis: that the formation of heterochromatin domains is mediated by phase separation, a phenomenon that gives rise to diverse non-membrane-bound nuclear, cytoplasmic and extracellular compartments4. We show that Drosophila HP1a protein undergoes liquid–liquid demixing in vitro, and nucleates into foci that display liquid properties during the first stages of heterochromatin domain formation in early Drosophila embryos. Furthermore, in both Drosophila and mammalian cells, heterochromatin domains exhibit dynamics that are characteristic of liquid phase-separation, including sensitivity to the disruption of weak hydrophobic interactions, and reduced diffusion, increased coordinated movement and inert probe exclusion at the domain boundary. We conclude that heterochromatic domains form via phase separation, and mature into a structure that includes liquid and stable compartments. We propose that emergent biophysical properties associated with phase-separated systems are critical to understanding the unusual behaviours of heterochromatin, and how chromatin domains in general regulate essential nuclear functions.

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confidence: 87%

Phase separation drives heterochromatin domain formation

Strom

Emelyanov

Mir

et al. 2017

Nature

1,525

1,422

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“…Our present understanding of basic principles that govern high-order genome organization can be attributed to incorporation of the physical properties of long-chain polymers [2][3][4][5][6][7]. The fluctuations of long-chain polymers, numerically simulated with Rouse-like bead-spring chain models of chromosomes confined to the nucleus, capture the tendency of chromosomes to self-associate and occupy territories [8][9][10][11] In addition, these models make predictions with regard to the spatial and dynamic timescales of inter-chromosomal interactions, a dynamic analog of topologically associated domains. The convergence of robust physical models with high-throughput biological data reveals the fractal nature of chromosome organization, namely an apparently self-similar cascade of loops within loops, or structure within structure, as one examines chromosomes at higher and higher resolution [12][13][14].…”

Section: Introductionmentioning

confidence: 99%

Transient crosslinking kinetics optimize gene cluster interactions

Walker

Taylor

Lawrimore

et al. 2019

Preprint

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Our understanding of how chromosomes structurally organize and dynamically interact has been revolutionized through the lens of long-chain polymer physics. Major protein contributors to chromosome structure and dynamics are condensin and cohesin that stochastically generate loops within and between chains, and entrap proximal strands of sister chromatids. In this paper, we explore the ability of transient, protein-mediated, gene-gene crosslinks to induce clusters of genes, thereby dynamic architecture, within the highly repeated ribosomal DNA that comprises the nucleolus of budding yeast. We implement three approaches: live cell microscopy; computational modeling of the full genome during G1 in budding yeast, exploring four decades of timescales for transient crosslinks between 5kbp domains (genes) in the nucleolus on Chromosome XII; and, temporal network models with automated community (cluster) detection algorithms applied to the full range of 4D modeling datasets. The data analysis tools detect and track gene clusters, their size, number, persistence time, and their plasticity (deformation). Of biological significance, our analysis reveals an optimal mean crosslink lifetime that promotes pairwise and cluster gene interactions through "flexible" clustering. In this state, large gene clusters self-assemble yet frequently interact (merge and separate), marked by gene exchanges between clusters, which in turn maximizes global gene interactions in the nucleolus. This regime stands between two limiting cases each with far less global gene interactions: with shorter crosslink lifetimes, "rigid" clustering emerges with clusters that interact infrequently; with longer crosslink lifetimes, there is a dissolution of clusters. These observations are compared with imaging experiments on a normal yeast strain and two condensin-modified mutant cell strains. We apply the same image analysis pipeline to the experimental and simulated datasets, providing support for the modeling predictions. Author SummaryThe spatiotemporal organization of the genome plays an important role in cellular processes involving DNA, but remains poorly understood, especially in the nucleolus, May 21, 2019 1/25 which does not facilitate conventional techniques. Polymer chain models have shown ability in recent years to make accurate predictions of the dynamics of the genome. We consider a polymer bead-chain model of the full yeast genome during the interphase portion of the cell cycle, featuring special dynamic crosslinking to model the effects of structural maintenance proteins in the nucleolus, and investigate how the kinetic timescale on which the crosslinks bind and unbind affects the resulting dynamics inside the nucleolus. It was previously known that when this timescale is sufficiently short, large, stable clusters appear, but when it is long, there is no resulting structure. We find that there additionally exists a range of timescales for which flexible clusters appear, in which beads frequently enter and leave clusters. Furthermore, we demonst...

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“…In metaphase, the loops emanate from a protein-rich chromosome scaffold. The chromosome scaffold is enriched in topology-adjusting proteins, such as topoisomerase II and the SMC (structural maintenance of chromosomes) proteins, known as condensin (Earnshaw et al 1985;Hirano 2006).Loops are a natural consequence of the entropic fluctuations and excluded volume interactions of tethered polymer chains in a confined space, such as the nucleus (Vasquez et al 2016). If we consider the genome as a ball of yarn, the formation of loops can be appreciated as chains that randomly collide and wiggle around one another.…”

mentioning

confidence: 99%

“…Loops are a natural consequence of the entropic fluctuations and excluded volume interactions of tethered polymer chains in a confined space, such as the nucleus (Vasquez et al 2016). If we consider the genome as a ball of yarn, the formation of loops can be appreciated as chains that randomly collide and wiggle around one another.…”

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confidence: 99%

RotoStep: A Chromosome Dynamics Simulator Reveals Mechanisms of Loop Extrusion

Lawrimore

Friedman

Doshi

et al. 2017

Cold Spring Harb Symp Quant Biol

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ChromoShake is a three-dimensional simulator designed to explore the range of configurational states a chromosome can adopt based on thermodynamic fluctuations of the polymer chain. Here, we refine ChromoShake to generate dynamic simulations of a DNA-based motor protein such as condensin walking along the chromatin substrate. We model walking as a rotation of DNAbinding heat-repeat proteins around one another. The simulation is applied to several configurations of DNA to reveal the consequences of mechanical stepping on taut chromatin under tension versus loop extrusion on single-tethered, floppy chromatin substrates. These simulations provide testable hypotheses for condensin and other DNA-based motors functioning along interphase chromosomes. Our model reveals a novel mechanism for condensin enrichment in the pericentromeric region of mitotic chromosomes. Increased condensin dwell time at centromeres results in a high density of pericentric loops that in turn provide substrate for additional condensin.There has been a revolution in understanding the higher-order structure and organization of chromosome in the past decade. Several major approaches (3C, ChromEMT, and super-resolution microscopy) are indicative of a disordered array of loopy fibers that emanate from an axial core (Dostie and Bickmore 2012;Dekker et al. 2013;Ou et al. 2017). The hierarchical models of structural intermediates building from 11 to 30 nm and larger fibers are not borne out in these recent 3D and live-cell studies (Ou et al. 2017). DNA looping was first observed in squash preparations of salamander eggs under the light microscope by the embryologist Oskar Hertwig in the early 1900s (Hertwig 1906). Paulson and Laemmli (1977) observed DNA loops when examining chromosome spreads in isolated mammalian cells. In metaphase, the loops emanate from a protein-rich chromosome scaffold. The chromosome scaffold is enriched in topology-adjusting proteins, such as topoisomerase II and the SMC (structural maintenance of chromosomes) proteins, known as condensin (Earnshaw et al. 1985;Hirano 2006).Loops are a natural consequence of the entropic fluctuations and excluded volume interactions of tethered polymer chains in a confined space, such as the nucleus (Vasquez et al. 2016). If we consider the genome as a ball of yarn, the formation of loops can be appreciated as chains that randomly collide and wiggle around one another. Energy-requiring processes are also involved in loop formation. The earliest suggestion of loop extrusion came from the trombone model of DNA replication (Sinha et al. 1980;Alberts et al. 1983) and direct visualization of DNA looping at the replication fork (Park et al. 1998). More recently, SMC proteins (e.g., cohesin and condensin), which bind and hydrolyze ATP, have been cited as having loop extrusion potential (Alipour and Marko 2012). Condensin has garnered attention based on recent studies showing it to be a DNA translocase (Terekawa et al. 2017).Condensin is composed of five subunits, two coiledcoils SMC2 and 4, a kleisin ...

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Entropy gives rise to topologically associating domains

Cited by 40 publications

References 80 publications

Phase separation drives heterochromatin domain formation

Phase separation drives heterochromatin domain formation

Transient crosslinking kinetics optimize gene cluster interactions

RotoStep: A Chromosome Dynamics Simulator Reveals Mechanisms of Loop Extrusion

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