Liquid-Liquid Phase Separation of Histone Proteins in Cells: Role in Chromatin Organization

Shakya, Anisha; Park, Seonyoung; Rana, Neha; King, John T.

doi:10.1016/j.bpj.2019.12.022

Cited by 124 publications

(134 citation statements)

References 69 publications

(112 reference statements)

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“…Even though the existence of charged disordered regions has been known for decades, we are only now starting to elucidate the physical basis underlying their functions. The physical properties of the charged disordered regions of H1 and the core histones are also likely to be crucial for processes involving liquid-liquid phase separation in chromatin 8,10,11,54,55 .…”

Section: Disorder Enables Histone Chaperoningmentioning

confidence: 99%

“…As a result, ProTα is expected to efficiently prevent nonspecific binding of H1 to DNA and ensure its targeting to the nucleosomal dyad.Finally, our results suggest that two long-standing questions in the chromatin field, namely the nature of the structural ensemble of H1 on the nucleosome 8 and the discrepancy between the residence times of H1 in vivo 31 and in vitro 33 , are closely connected: It may be precisely the large degree of structural disorder and long-range dynamics in the tails of nucleosome-bound H1 that enable chaperones such as ProTα to invade the H1/nucleosome complex and in this way accelerate H1 dissociation by competitive substitution instead of passively scavenging H1 once dissociated. Related processes involving charged disordered proteins may affect many aspects of chromatin assembly and dynamics, and cellular regulation in general 10,11,26,55 .…”

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confidence: 99%

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Disordered Proteins Enable Histone Chaperoning on the Nucleosome

Heidarsson

Mercadante

Sottini

et al. 2020

Preprint

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Proteins with highly charged disordered regions are abundant in the nucleus, where many of them interact with nucleic acids and control key processes such as transcription. The functional advantages conferred by protein disorder, however, have largely remained unclear. Here we show that disorder can facilitate a remarkable regulatory mechanism involving molecular competition. Single-molecule experiments demonstrate that the human linker histone H1 binds to the nucleosome with ultra-high affinity. However, the large-amplitude dynamics of the positively charged disordered regions of H1 persist on the nucleosome and facilitate the interaction with the highly negatively charged and disordered histone chaperone prothymosin α. Consequently, prothymosin α can efficiently invade the H1-nucleosome complex and displace H1 via competitive substitution. By integrating experiments and simulations, we establish a molecular model that rationalizes this process structurally and kinetically. Given the abundance of charged disordered regions in the nuclear proteome, this mechanism may be widespread in cellular regulation. 3 A large fraction of the human genome codes for proteins that contain substantial disordered regions or even lack any well-defined three-dimensional structure 1 . These intrinsically disordered proteins are involved in many cellular processes and mediate key interactions with other proteins or nucleic acids 2 . DNA-and RNA-binding proteins often contain disordered regions highly enriched in positively charged residues 3,4 , which are expected to facilitate electrostatic interactions with their cellular targets, the highly negatively charged nucleic acids 3 . The affinities can be remarkably high, even if no structure is formed upon binding 5,6 . Such polyelectrolyte interactions have long been known in the field of soft matter physics 7 , but their importance in biology has only recently started to be recognized 5,6,[8][9][10][11] and is thus largely unexplored.A ubiquitous group of proteins with long disordered positively charged regions are the histones, which are responsible for packaging DNA into chromatin. Among these, the linker histones are particularly remarkable 12 : They are largely disordered and highly positively charged, with two disordered regions flanking a small folded globular domain. By binding to the linker DNA on the nucleosome (Fig. 1a), linker histones contribute to chromatin condensation and transcriptional regulation 12,13 . However, the role of protein disorder in the complex between nucleosome and linker histone and the functional consequences have remained unclear. Here, by integrating single-molecule experiments and simulations, we establish a molecular model of the linker histone-nucleosome complex and show that disorder enables an unexpected mechanism that regulates linker histone binding: The highly negatively charged and disordered human protein prothymosin α (ProTα), a histone chaperone 14-17 that forms a high-affinity disordered complex with linker histone H1 5 , can efficiently...

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Section: Disorder Enables Histone Chaperoningmentioning

confidence: 99%

mentioning

confidence: 99%

Disordered Proteins Enable Histone Chaperoning on the Nucleosome

Heidarsson

Mercadante

Sottini

et al. 2020

Preprint

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“…Over the past decade, several research groups have suggested that the mechanism of formation of membraneless organelles can be explained in terms of phase separation (liquidliquid phase separation, LLPS) (Jacobs and Frenkel 2017;Schuster et al 2018;Alberti et al 2019;Shakya et al 2020;Klosin et al 2020). In the cytosol, interactions can also occur among specific proteinous and nucleic acid polymers, and thus it is worth examining which domains of both molecules are important for the generation of microdroplets segregated from their surroundings upon LLPS.…”

Section: Introductionmentioning

confidence: 99%

Nonspecific characteristics of macromolecules create specific effects in living cells

et al. 2020

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Recently, the important role of microphase separation in living cells has been attracting considerable interest in relation to cell organization and function. For example, many studies have focused on liquid-liquid phase separation (LLPS) as a very plausible mechanism for the presence of membraneless organelles. To confirm the role of phase separation in living cells, experimental studies on models and/or reconstructed systems are needed. In this short review, we discuss current paradigms of LLPS and provide some example "review data" to demonstrate particular points relating to the specific localization of biological macromolecules like DNAs and actin proteins with spontaneous domain formation in microdroplets emerging in an aqueous two-phase system (ATPS) (we use polyethylene glycol (PEG)/dextran (DEX)-a binary polymer solution). We also suggest that phase separation and transition may play basic roles in regulation of the biochemical reactivity of individual long genomic DNAs.

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“…This process is typically referred to as seeding nucleation of condensate formation [ 9 ]. The organizing platform may be a protein [ 22 , 23 ], RNA [ 24 , 25 ], polyADP-ribose [ 26 ], DNA [ 27 , 28 ], or chromatin fibril [ 28 ]. The phase condensates generated by LLPS are expected to possess a round shape, fuse upon coalescence, and quickly exchange components with the external milieu [ 29 , 30 ].…”

Section: Introductionmentioning

confidence: 99%

Divide and Rule: Phase Separation in Eukaryotic Genome Functioning

Razin

Ulianov

2020

Cells

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The functioning of a cell at various organizational levels is determined by the interactions between macromolecules that promote cellular organelle formation and orchestrate metabolic pathways via the control of enzymatic activities. Although highly specific and relatively stable protein-protein, protein-DNA, and protein-RNA interactions are traditionally suggested as the drivers for cellular function realization, recent advances in the discovery of weak multivalent interactions have uncovered the role of so-called macromolecule condensates. These structures, which are highly divergent in size, composition, function, and cellular localization are predominantly formed by liquid-liquid phase separation (LLPS): a physical-chemical process where an initially homogenous solution turns into two distinct phases, one of which contains the major portion of the dissolved macromolecules and the other one containing the solvent. In a living cell, LLPS drives the formation of membrane-less organelles such as the nucleolus, nuclear bodies, and viral replication factories and facilitates the assembly of complex macromolecule aggregates possessing regulatory, structural, and enzymatic functions. Here, we discuss the role of LLPS in the spatial organization of eukaryotic chromatin and regulation of gene expression in normal and pathological conditions.

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Liquid-Liquid Phase Separation of Histone Proteins in Cells: Role in Chromatin Organization

Cited by 124 publications

References 69 publications

Disordered Proteins Enable Histone Chaperoning on the Nucleosome

Disordered Proteins Enable Histone Chaperoning on the Nucleosome

Nonspecific characteristics of macromolecules create specific effects in living cells

Divide and Rule: Phase Separation in Eukaryotic Genome Functioning

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