DNA looping mediates nucleosome transfer

Brennan, Lucy D.; Forties, Robert A.; Patel, Smita S.; Wang, Michelle D.

doi:10.1038/ncomms13337

Cited by 42 publications

(27 citation statements)

References 69 publications

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“…Transfer of the nucleosome core from one DNA substrate to another, as illustrated in Figure 5 , is another characteristic of CENP-A nucleosomes that has not been directly visualized before. Evidence of interstrand nucleosome transfer was presented and discussed in landmark studies ( 32 , 33 ) and was recently demonstrated in a magnetic tweezers study ( 34 ). Furthermore, our results directly support such an ability.…”

Section: Discussionmentioning

confidence: 95%

Nanoscale dynamics of centromere nucleosomes and the critical roles of CENP-A

Stumme-Diers

Banerjee

Hashemi

et al. 2017

Nucleic Acids Research

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In the absence of a functioning centromere, chromosome segregation becomes aberrant, leading to an increased rate of aneuploidy. The highly specific recognition of centromeres by kinetochores suggests that specific structural characteristics define this region, however, the structural details and mechanism underlying this recognition remains a matter of intense investigation. To address this, high-speed atomic force microscopy was used for direct visualization of the spontaneous dynamics of CENP-A nucleosomes at the sub-second time scale. We report that CENP-A nucleosomes change conformation spontaneously and reversibly, utilizing two major pathways: unwrapping, and looping of the DNA; enabling core transfer between neighboring DNA substrates. Along with these nucleosome dynamics we observed that CENP-A stabilizes the histone core against dissociating to histone subunits upon unwrapping DNA, unique from H3 cores which are only capable of such plasticity in the presence of remodeling factors. These findings have implications for the dynamics and integrity of nucleosomes at the centromere.

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Section: Discussionmentioning

confidence: 95%

Nanoscale dynamics of centromere nucleosomes and the critical roles of CENP-A

Stumme-Diers

Banerjee

Hashemi

et al. 2017

Nucleic Acids Research

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“…2c) (43). In line with these observations, studies using optical tweezers have demonstrated that T7 helicase can displace DNA-bound proteins, such as a nucleosome or RNA polymerase (RNAP), under the assistance of an external force, indicating that helicase might clear away roadblocks during replication (25,44,45). In some cases, the replisome may rely on obstacles to terminate replication.…”

Section: Replicative Helicases Unwind Through Obstaclesmentioning

confidence: 77%

Rescuing Replication from Barriers: Mechanistic Insights from Single-Molecule Studies

Sun

2019

Molecular and Cellular Biology

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To prevent replication failure due to fork barriers, several mechanisms have evolved to restart arrested forks independent of the origin of replication. Our understanding of these mechanisms that underlie replication reactivation has been aided through unique dynamic perspectives offered by single-molecule techniques. These techniques, such as optical tweezers, magnetic tweezers, and fluorescencebased methods, allow researchers to monitor the unwinding of DNA by helicase, nucleotide incorporation during polymerase synthesis, and replication fork progression in real time. In addition, they offer the ability to distinguish DNA intermediates after obstacles to replication at high spatial and temporal resolutions, providing new insights into the replication reactivation mechanisms. These and other highlights of single-molecule techniques and remarkable studies on the recovery of the replication fork from barriers will be discussed in this review.

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“…Unzipping DNA reveals a detailed and distinct force signature shaped by the underlying energy landscape of its sequence, and thus unzipping also serves as a powerful tool for probing and localizing protein-DNA interactions 5,[25][26][27] . A bound protein presents a roadblock which increases resistance to unzipping, resulting in a detectable rise in force above the naked DNA baseline when the unzipping fork encounters the protein.…”

Section: Fork Breathing Fluctuations Modulate Protein Unzippingmentioning

confidence: 99%

“…The generation of stretching and unzipping templates has been described previously 25,39,40 . For forming DNA dumbbell tethers, carboxylated beads (Polysciences) were coated with (either) streptavidin and anti-digoxigenin in house.…”

Section: Stretching and Unzipping Experimentsmentioning

confidence: 99%

High-Performance Image-Based Measurements of Biological Forces and Interactions in a Dual Optical Trap

Inman

Wang

2018

Preprint

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Optical traps enable nanoscale manipulation of individual biomolecules while measuring molecular forces and lengths. This ability relies on the sensitive detection of optically trapped particles, typically accomplished using laser-based interferometric methods. Recently, precise and fast image-based particle tracking techniques have garnered increased interest as a potential alternative to laser-based detection, however successful integration of image-based methods into optical trapping instruments for biophysical applications and force measurements has remained elusive. Here we develop a camera-based detection platform that enables exceptionally accurate and precise measurements of biological forces and interactions in a dual optical trap. In demonstration, we stretch and unzip DNA molecules while measuring the relative distances of trapped particles from their trapping centers with sub-nanometer accuracy and precision, a performance level previously only achieved using photodiodes. We then use the DNA unzipping technique to localize bound proteins with extraordinary sub-base-pair precision, revealing how thermal DNA fluctuations allow an unzipping fork to sense and respond to a bound protein prior to a direct encounter. This work significantly advances the capabilities of image tracking in optical traps, providing a state-of-the-art detection method that is accessible, highly flexible, and broadly compatible with diverse experimental substrates and other nanometric techniques.

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DNA looping mediates nucleosome transfer

Cited by 42 publications

References 69 publications

Nanoscale dynamics of centromere nucleosomes and the critical roles of CENP-A

Nanoscale dynamics of centromere nucleosomes and the critical roles of CENP-A

Rescuing Replication from Barriers: Mechanistic Insights from Single-Molecule Studies

High-Performance Image-Based Measurements of Biological Forces and Interactions in a Dual Optical Trap

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