Liquid-like behavior of chromatin

Maeshima, Kazuhiro; Ide, Satoru; Hibino, Kayo; Sasai, Masaki

doi:10.1016/j.gde.2015.11.006

Cited by 129 publications

(116 citation statements)

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“…A more dynamic, liquid-like state of chromatin is currently considered ( 48 ) instead of the classical 30-nm fibers, which so far have not been observed in vivo. A dynamic, “fluid” behavior of chromatin would be fully supported by the weak nucleosome-nucleosome interaction potential measured here.…”

Section: Discussionmentioning

confidence: 99%

Uncovering the forces between nucleosomes using DNA origami

et al. 2016

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Section: Discussionmentioning

confidence: 99%

Uncovering the forces between nucleosomes using DNA origami

et al. 2016

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“…In fact, micromechanical experiments using micropipettes have shown that mitotic chromosomes are highly elastic objects that return to their native lengths even after five-fold extensions (Marko, 2008). Compared with the interior of chromosomes, their periphery is expected to be less dense and to behave like a liquid, as has been predicted for interphase chromatin (Maeshima et al, 2016). Along these lines, an intriguing observation from an early study is that the condensin subunit SMC2 first appears at the surface of condensing chromosomes in middle prophase, and then suddenly translocates into the interior of chromosomes where axial structures are formed by late prophase (Kireeva et al, 2004) (Fig.…”

Section: Heat Repeats In Mitotic Chromosome Dynamicsmentioning

confidence: 96%

HEAT repeats – versatile arrays of amphiphilic helices working in crowded environments?

Yoshimura

Hirano

2016

Journal of Cell Science

129

121

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Cellular proteins do not work in isolation. Instead, they often function as part of large macromolecular complexes, which are transported and concentrated into specific cellular compartments and function in a highly crowded environment. A central theme of modern cell biology is to understand how such macromolecular complexes are assembled efficiently and find their destinations faithfully. In this Opinion article, we will focus on HEAT repeats, flexible arrays of amphiphilic helices found in many eukaryotic proteins, such as karyopherins and condensins, and discuss how these uniquely designed helical repeats might underlie dynamic protein-protein interactions and support cellular functions in crowded environments. We will make bold speculations on functional similarities between the action of HEAT repeats and intrinsically disordered regions (IDRs) in macromolecular phase separation. Potential contributions of HEAT-HEAT interactions, as well as cooperation between HEATs and IDRs, to mesoscale organelle assembly will be discussed.

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“…(31,32,70,71). Additionally, several theoretical models (72)(73)(74)(75) and computer simulations of chromatin polymer (17,34,34,61,76) have shown the broad consistency of heterogeneous copolymer melt view of chromatin with the Hi-C and single-molecule data.…”

Section: Resultsmentioning

confidence: 88%

Mesoscale liquid model of chromatin recapitulates nuclear order of eukaryotes

Laghmach

Pierro

Potoyan

2019

Preprint

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The nuclear envelope segregates the genome of Eukaryota from the cytoplasm. Within the nucleus, chromatin is further compartmentalized into architectures that change throughout the lifetime of the cell. Epigenetic patterns along the chromatin polymer strongly correlate with chromatin compartmentalization and, accordingly, also change during the cell life cycle and at differentiation. Recently, it has been suggested that sub-nuclear chromatin compartmentalization might result from a process of liquid-liquid phase separation orchestrated by the epigenetic marking and operated by proteins that bind to chromatin. Here, we translate these observations into a diffuse interface model of chromatin, which we named MEsoscale Liquid mOdel of Nucleus (MELON). Using this streamlined continuum model of the genome, we study the large-scale rearrangements of chromatin that happen at different stages of the growth and senescence of the cell, and during nuclear inversion events. Particularly, we investigate the role of droplet diffusion, fluctuations, and heterochromatin-lamina interactions during nuclear remodeling. Our results indicate that the physical process of liquid-liquid phase separation, together with surface effects is sufficient to recapitulate much of the large-scale morphology and dynamics of chromatin along the life cycle of cells. SIGNIFICANCE STATEMENTEukaryotic chromatin occupies a few micrometers of nuclear space while remaining dynamic and accessible for gene regulation. The physical state of nuclear chromatin is shaped by the juxtaposition of complex, out of equilibrium processes on one hand and intrinsic polymeric aspect of the genome on the other. Recent experiments have revealed a remarkable ability of disordered nuclear proteins to drive liquid-liquid phase separation of chromatin domains. We have built a mesoscale liquid model of nuclear chromatin which allows dissecting the contribution of liquid behavior of chromatin to nuclear order of eukaryotes. Our results show that liquid-liquid phase separation, together with surface effects is sufficient for recapitulating large-scale morphology and dynamics of chromatin at many stages of the nuclear cycle. Laghmach et alClear evidence of hierarchical compartmentalization in chromatin at multiple scales has emerged through studies employing DNA-DNA proximity ligation assays. First, two genomic compartments were observed (3), named A and B, which were then refined through higher resolution experiments to reveal the existence of even smaller sub-compartments (10). The A and B compartments appear to be enriched in epigenetic markings correlating with transcriptional activation and silencing respectively. Several studies have suggested that chromatin compartmentalization may result from a process of liquid-liquid phase separation orchestrated by the epigenetic markings which collectively act to remodel chromosomal loci (15)(16)(17)(18)(19). The epigenetically driven phase segregation events have shown to emerge right at the nucleosome resolution mediated by protein b...

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Liquid-like behavior of chromatin

Cited by 129 publications

References 100 publications

Uncovering the forces between nucleosomes using DNA origami

Uncovering the forces between nucleosomes using DNA origami

HEAT repeats – versatile arrays of amphiphilic helices working in crowded environments?

Mesoscale liquid model of chromatin recapitulates nuclear order of eukaryotes

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