Chromatin remodeling by ISW2 and SWI/SNF requires DNA translocation inside the nucleosome

@article{Zofall2006ChromatinRB,
  title={Chromatin remodeling by ISW2 and SWI/SNF requires DNA translocation inside the nucleosome},
  author={Martin Zofall and Jim Persinger and Stefan R. Kassabov and Blaine Bartholomew},
  journal={Nature Structural \&Molecular Biology},
  year={2006},
  volume={13},
  pages={339-346}
}
Chromatin-remodeling complexes regulate access to nucleosomal DNA by mobilizing nucleosomes in an ATP-dependent manner. In this study, we find that chromatin remodeling by SWI/SNF and ISW2 involves DNA translocation inside nucleosomes two helical turns from the dyad axis at superhelical location-2. DNA translocation at this internal position does not require the propagation of a DNA twist from the site of translocation to the entry/exit sites for nucleosome movement. Nucleosomes are moved in 9… 
SWI/SNF- and RSC-Catalyzed Nucleosome Mobilization Requires Internal DNA Loop Translocation within Nucleosomes
TLDR
This work test the idea that remodeling involves intermediates with mobile DNA bulges or loops within the nucleosome by cross-linking the H2A N- or C-terminal tails together to generate protein “loops” that constrict separation of the DNA from the histone surface, and proposes a threading model for movement of DNA loops around the perimeter of theucleosome core.
Probing SWI/SNF remodeling of the nucleosome by unzipping single DNA molecules
TLDR
Nucleosomes remodeled by yeast SWI/SNF were moved bidirectionally along the DNA, resulting in a continuous position distribution, indicating that their overall structure remained canonical.
Stepwise nucleosome translocation by RSC remodeling complexes
TLDR
Single-molecule FRET is used to monitor the remodeling of mononucleosomes by the yeast SWI/SNF remodeler, RSC, and results suggest that the movement of DNA across the nucleosome is likely coupled directly to DNA translocation by the ATPase at its binding site inside theucleosome.
Architecture of the SWI/SNF-Nucleosome Complex
TLDR
The model of the binding trough of SWI/SNF illustrates how nucleosomal DNA can be mobilized while SWI-SNF remains bound.
The SnAC Domain of SWI/SNF Is a Histone Anchor Required for Remodeling
TLDR
The role of another domain in Snf2 called SnAC (Snf2 ATP coupling) that was shown previously to regulate the ATPase activity of SWI/SNF is examined and it is found that deletion of the SnAC domain strongly uncouples ATP hydrolysis from nucleosome movement.
Multiple Aspects of ATP-Dependent Nucleosome Translocation by RSC and Mi-2 Are Directed by the Underlying DNA Sequence
TLDR
A successive three-step framework consisting of initiation, translocation and release steps to describe SNF2-type enzyme mediated nucleosome translocation along DNA helps resolve the apparent paradox between the high abundance of ATP-dependent remodelers per nucleus and the relative success of sequence-based predictions of nucleosite positioning in vivo.
The INO80 ATP-Dependent Chromatin Remodeling Complex Is a Nucleosome Spacing Factor † † Supplemental material for this article may be found at http://dx.doi.org/10.1128/MCB.01035-10.
TLDR
INO80 prefers to move mononucleosomes to the center of DNA, like ISW2 and ISW1a, but does so with higher precision, and requires a minimum length of 33 to 43 bp of extranucleosomal DNA for mobilizing nucleosomes, with 70 bp being optimal.
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References

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TLDR
DNA photoaffinity labeling of RSC showed that the Rsc4 subunit is in close proximity to nucleosomal DNA and not when RSC is bound to free DNA, indicating significant changes in SWI/SNF and RSC contacts with DNA after remodeling.
hSWI/SNF-Catalyzed Nucleosome Sliding Does Not Occur Solely via a Twist-Diffusion Mechanism
TLDR
It is reported that hSWI/SNF efficiently catalyzes sliding of nucleosomes containing branched DNAs as steric blocks to twist-diffusion and a nick to allow dissipation of torsional stress within the nucleosome.
Chromatin remodeling through directional DNA translocation from an internal nucleosomal site
TLDR
Results with various nucleosome substrates suggest that RSC/Sth1 remains at a fixed position on the histone octamer and that Sth1 conducts directional DNA translocation from a location about two turns from the nucleosomal dyad, drawing in DNA from one side of the nucleOSome and pumping it toward the other.
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TLDR
It is proposed that the remodeling enzyme remains in a fixed position on the octamer and translocates a segment of DNA (with accompanying DNA twist), which breaks histone-DNA contacts and propagates as a wave of DNA around theOctamer.
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TLDR
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TLDR
Kinetic analysis reveals that nucleosome sliding occurs in apparent increments or steps of 10 bp, and these findings support a sliding model in which the position-specific tethering of NURF forces a translocating ISWI ATPase to pump a DNA distortion over the histone octamer, thereby changing the translational position of the nucleosomes.
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TLDR
In conclusion, indications are that the extranucleosomal DNA immediately adjacent to the nucleosome has an important role in the initial stage of nucleosomes movement by ISW2.
High-Resolution Mapping of Changes in Histone-DNA Contacts of Nucleosomes Remodeled by ISW2
ABSTRACT The imitation switch (ISWI) complex from yeast containing the Isw2 and Itc1 proteins was shown to preferentially slide mononucleosomes with as little as 23 bp of linker DNA from the end to
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