ATP-dependent remodeling of chromatin condensates reveals distinct mesoscale outcomes.
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| Title: | ATP-dependent remodeling of chromatin condensates reveals distinct mesoscale outcomes. |
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| Authors: | Moore, Camille, Wong, Emily, Kaur, Upneet, Chio, Un Seng, Zhou, Ziling, Ostrowski, Megan, Wu, Ke, Irkliyenko, Iryna, Wang, Sean, Ramani, Vijay, Narlikar, Geeta J. |
| Source: | Science. 10/2/2025, Vol. 390 Issue 6768, p1-12. 12p. |
| Subjects: | Adenosine triphosphate, Chromatin, Condensation reactions, Genetic transcription, Valence (Chemistry) |
| Abstract: | Adenosine triphosphate (ATP)–dependent chromatin remodeling enzymes mobilize nucleosomes, but how such mobilization affects chromatin condensation is unclear. We investigate effects of two major remodelers, ACF and RSC, using chromatin condensates and single-molecule footprinting. We find that both remodelers inhibit the formation of condensed chromatin. However, the remodelers have distinct effects on preformed chromatin condensates. ACF spaces nucleosomes without decondensing the chromatin, explaining how ACF maintains nucleosome organization in transcriptionally repressed genomic regions. By contrast, RSC catalyzes ATP-dependent decondensation of chromatin. RSC also drives micron-scale movements of entire chromatin condensates. These additional activities of RSC may contribute to its central role in transcription. The biological importance of remodelers may thus reflect both their effects on nucleosome mobilization and the corresponding consequences on chromatin dynamics at the mesoscale. Editor's summary: Eukaryotic DNA is packaged as chromatin, the basic unit of which is the nucleosome, around which about 150 base pairs of DNA are wrapped, limiting its accessibility. Chromatin remodelers mobilize nucleosomes to regulate replication and transcription. Moore et al. studied two major remodelers, ACF and RSC, in crowded chromatin by recreating phase-separated chromatin droplets in vitro. They found that both remodelers could enter and mobilize nucleosomes within droplets, but only RSC decompacted chromatin and increased droplet mobility. This decompaction likely enhances DNA accessibility in cells. Their findings suggest that remodelers differ in biological importance depending on their capacity to mobilize and decompact compacted chromatin. —Di Jiang INTRODUCTION: Adenosine triphosphate (ATP)–dependent chromatin remodelers can slide, disassemble, deform, and space nucleosomes. However, each remodeler has a distinct impact on nucleosomes. For example, the imitation switch remodeler ACF has been shown to generate the evenly spaced nucleosome architecture found in heterochromatin. By contrast, the switch/sucrose nonfermentable remodeler RSC slides, deforms, and disassembles nucleosomes and is critical for enabling DNA access in euchromatin. Most of our mechanistic understanding of remodeler action derives from detailed studies at the nucleosome scale. At the genomic scale, studies have shown correlations between specific remodelers and changes in chromatin organization in cells. However, whether and how the action of chromatin remodelers at the nucleosome scale affects chromatin dynamics at the mesoscale remains an open question. RATIONALE: In cells, remodelers must operate within a crowded chromatin environment with estimated nucleosome concentrations of ~100 µM or higher. How chromatin remodelers act in such a crowded environment is poorly understood. A simple prediction is that ATP-driven nucleosome mobilization disrupts interactions between nucleosomes, resulting in local chromatin decondensation. Thus, remodelers may act as molecular "stir bars." Previous work has shown that chromatin compacts into phase-separated condensates in vitro. These condensates have nucleosome concentrations comparable to those within the nucleus. We build on these studies to ask how two key remodelers ACF and RSC—which carry out substantially different transformations of a nucleosome—contend with a crowded chromatin environment. Further, as chromatin varies in nucleosome density and spacing in cells, we also investigate how nucleosome spacing and density affect chromatin condensation. RESULTS: To investigate the interplay between condensed chromatin and remodelers, we reconstituted chromatin in vitro on a genomic DNA sequence and combined confocal imaging of chromatin condensates with single-molecule footprinting of chromatin fibers. We found that increasing the density of nucleosomes promoted phase separation after controlling for total nucleosome concentration, consistent with increased nucleosomal valency promoting chromatin condensation. The condensates were also highly viscous. However, despite the high viscosity of the chromatin condensates, ACF and RSC could still remodel nucleosomes within this environment and each remodeler generated similar products as observed previously with uncondensed chromatin. Remodeling by ACF does not substantially affect chromatin condensation whereas remodeling by RSC decondenses the chromatin. RSC-mediated nucleosome occlusion and RSC-remodeled chromatin products both drive chromatin decondensation. The extent of the occlusion effect depends on the molar ratio of RSC:nucleosome. Furthermore, RSC activity promotes micron-scale motions of entire condensates, unlike ACF. This additional RSC activity may reduce the local chromatin viscosity and enable faster diffusion of transcriptional factors in cells. CONCLUSION: Our findings demonstrate that ATP-dependent remodelers do not generically act as molecular stir bars; rather, their mesoscale effects on chromatin derive from their specific, nucleosome-scale interactions and activities. The biological importance of remodelers may thus reflect both their effects on nucleosome mobilization and the corresponding consequences on chromatin dynamics at the mesoscale. Future work is needed to clarify whether other nucleosome remodelers that catalyze distinct transformations of nucleosomes also have distinct effects on meso-scale chromatin dynamics. Effects of ATP-dependent chromatin remodelers on mesoscale chromatin organization and dynamics in vitro.: Both ACF and RSC can remodel nucleosomes within chromatin condensates. Remodeling by ACF does not substantially affect chromatin condensation whereas remodeling by RSC decondenses chromatin. RSC-mediated nucleosome occlusion and RSC-remodeled chromatin products both drive chromatin decondensation. [ABSTRACT FROM AUTHOR] |
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| Database: | Psychology and Behavioral Sciences Collection |
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| Abstract: | Adenosine triphosphate (ATP)–dependent chromatin remodeling enzymes mobilize nucleosomes, but how such mobilization affects chromatin condensation is unclear. We investigate effects of two major remodelers, ACF and RSC, using chromatin condensates and single-molecule footprinting. We find that both remodelers inhibit the formation of condensed chromatin. However, the remodelers have distinct effects on preformed chromatin condensates. ACF spaces nucleosomes without decondensing the chromatin, explaining how ACF maintains nucleosome organization in transcriptionally repressed genomic regions. By contrast, RSC catalyzes ATP-dependent decondensation of chromatin. RSC also drives micron-scale movements of entire chromatin condensates. These additional activities of RSC may contribute to its central role in transcription. The biological importance of remodelers may thus reflect both their effects on nucleosome mobilization and the corresponding consequences on chromatin dynamics at the mesoscale. Editor's summary: Eukaryotic DNA is packaged as chromatin, the basic unit of which is the nucleosome, around which about 150 base pairs of DNA are wrapped, limiting its accessibility. Chromatin remodelers mobilize nucleosomes to regulate replication and transcription. Moore et al. studied two major remodelers, ACF and RSC, in crowded chromatin by recreating phase-separated chromatin droplets in vitro. They found that both remodelers could enter and mobilize nucleosomes within droplets, but only RSC decompacted chromatin and increased droplet mobility. This decompaction likely enhances DNA accessibility in cells. Their findings suggest that remodelers differ in biological importance depending on their capacity to mobilize and decompact compacted chromatin. —Di Jiang INTRODUCTION: Adenosine triphosphate (ATP)–dependent chromatin remodelers can slide, disassemble, deform, and space nucleosomes. However, each remodeler has a distinct impact on nucleosomes. For example, the imitation switch remodeler ACF has been shown to generate the evenly spaced nucleosome architecture found in heterochromatin. By contrast, the switch/sucrose nonfermentable remodeler RSC slides, deforms, and disassembles nucleosomes and is critical for enabling DNA access in euchromatin. Most of our mechanistic understanding of remodeler action derives from detailed studies at the nucleosome scale. At the genomic scale, studies have shown correlations between specific remodelers and changes in chromatin organization in cells. However, whether and how the action of chromatin remodelers at the nucleosome scale affects chromatin dynamics at the mesoscale remains an open question. RATIONALE: In cells, remodelers must operate within a crowded chromatin environment with estimated nucleosome concentrations of ~100 µM or higher. How chromatin remodelers act in such a crowded environment is poorly understood. A simple prediction is that ATP-driven nucleosome mobilization disrupts interactions between nucleosomes, resulting in local chromatin decondensation. Thus, remodelers may act as molecular "stir bars." Previous work has shown that chromatin compacts into phase-separated condensates in vitro. These condensates have nucleosome concentrations comparable to those within the nucleus. We build on these studies to ask how two key remodelers ACF and RSC—which carry out substantially different transformations of a nucleosome—contend with a crowded chromatin environment. Further, as chromatin varies in nucleosome density and spacing in cells, we also investigate how nucleosome spacing and density affect chromatin condensation. RESULTS: To investigate the interplay between condensed chromatin and remodelers, we reconstituted chromatin in vitro on a genomic DNA sequence and combined confocal imaging of chromatin condensates with single-molecule footprinting of chromatin fibers. We found that increasing the density of nucleosomes promoted phase separation after controlling for total nucleosome concentration, consistent with increased nucleosomal valency promoting chromatin condensation. The condensates were also highly viscous. However, despite the high viscosity of the chromatin condensates, ACF and RSC could still remodel nucleosomes within this environment and each remodeler generated similar products as observed previously with uncondensed chromatin. Remodeling by ACF does not substantially affect chromatin condensation whereas remodeling by RSC decondenses the chromatin. RSC-mediated nucleosome occlusion and RSC-remodeled chromatin products both drive chromatin decondensation. The extent of the occlusion effect depends on the molar ratio of RSC:nucleosome. Furthermore, RSC activity promotes micron-scale motions of entire condensates, unlike ACF. This additional RSC activity may reduce the local chromatin viscosity and enable faster diffusion of transcriptional factors in cells. CONCLUSION: Our findings demonstrate that ATP-dependent remodelers do not generically act as molecular stir bars; rather, their mesoscale effects on chromatin derive from their specific, nucleosome-scale interactions and activities. The biological importance of remodelers may thus reflect both their effects on nucleosome mobilization and the corresponding consequences on chromatin dynamics at the mesoscale. Future work is needed to clarify whether other nucleosome remodelers that catalyze distinct transformations of nucleosomes also have distinct effects on meso-scale chromatin dynamics. Effects of ATP-dependent chromatin remodelers on mesoscale chromatin organization and dynamics in vitro.: Both ACF and RSC can remodel nucleosomes within chromatin condensates. Remodeling by ACF does not substantially affect chromatin condensation whereas remodeling by RSC decondenses chromatin. RSC-mediated nucleosome occlusion and RSC-remodeled chromatin products both drive chromatin decondensation. [ABSTRACT FROM AUTHOR] |
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| ISSN: | 00368075 |
| DOI: | 10.1126/science.adr0018 |
