Conformational Changes Associated with Template Commitment in ATP-Dependent Chromatin Remodeling by ISW2

Gangaraju, Vamsi K.; Prasad, Punit; Srour, Ali; Kagalwala, Mohamedi N.; Bartholomew, Blaine

doi:10.1016/j.molcel.2009.05.013

Cited by 49 publications

(63 citation statements)

References 28 publications

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“…It is noted that such a small step size would be in contradiction to the experimentally observed remodeling behavior of ISWI remodelers, for which translocation steps of ∼10-50 bp were reported (30). In addition, the ACF complex has been shown to be committed to its substrate for several minutes in vitro, further supporting the notion that the remodeling reaction does not occur within <150 ms (41,42). Thus, we conclude that the 96-97% mobile remodeler fraction found here is not engaged in chromatin remodeling under "housekeeping" conditions in G1/2 phase.…”

Section: Discussionmentioning

confidence: 81%

Human ISWI chromatin-remodeling complexes sample nucleosomes via transient binding reactions and become immobilized at active sites

Erdel

Schubert

Marth

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

109

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Chromatin remodeling complexes can translocate nucleosomes along the DNA in an ATP-dependent manner. Here, we studied autofluorescent protein constructs of the human ISWI family members Snf2H, Snf2L, the catalytically inactive Snf2L+13 splice variant, and the accessory Acf1 subunit in living human and mouse cells by fluorescence microscopy/spectroscopy. Except for Snf2L, which was not detected in the U2OS cell line, the endogenous ISWI proteins were abundant at nuclear concentrations between 0.14 and 0.83 μM. A protein interaction analysis showed the association of multimeric Snf2H and Acf1 into a heterotetramer or higher-order ACF complex. During the G1/2 cell cycle phase, Snf2H and Snf2L displayed average residence times <150 ms in the chromatin-bound state. The comparison of active and inactive Snf2H/Snf2L indicated that an immobilized fraction potentially involved in active chromatin remodeling comprised only 1-3%. This fraction was largely increased at replication foci in S phase or at DNA repair sites. To rationalize these findings we propose that ISWI remodelers operate via a "continuous sampling" mechanism: The propensity of nucleosomes to be translocated is continuously tested in transient binding reactions. Most of these encounters are unproductive and efficient remodeling requires an increased binding affinity to chromatin. Due to the relatively high intranuclear remodeler concentrations cellular response times for repositioning a given nucleosome were calculated to be in the range of tens of seconds to minutes.nucleosome translocation | fluorescence recovery after photobleaching | fluorescence correlation spectroscopy

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Section: Discussionmentioning

confidence: 81%

Human ISWI chromatin-remodeling complexes sample nucleosomes via transient binding reactions and become immobilized at active sites

Erdel

Schubert

Marth

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

109

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“…These findings are as follows: 1) Previous work has shown that the ATPase domain of ISWI enzymes engages the histone H4 tail (Mueller-Planitz et al, 2013) and the surrounding nucleosomal DNA at super-helical location 2 (SHL2; Dang and Bartholomew, 2007) in the apo state. We have previously reported that SNF2h engages the H4 tail and SHL2 DNA in both the apo and ADP-BeF x states (Racki et al, 2009), and others have observed that the homologous yeast ISW2 protects this location in the apo and ADP states (Gangaraju et al, 2009). These previous findings suggest that the ATPase domain remains engaged at SHL2 in the apo, ADP and ADP-BeF x states.…”

Section: Discussionmentioning

confidence: 95%

“…One study of the homologous yeast ISW2 complex reported the appearance of a new region of protection on nucleosomal DNA shortly following the addition of ATP or during remodeling of stalled nucleosomes (Gangaraju et al, 2009). This protected region overlaps with our two internal FRET probes (Figure 3), and we have previously observed increased protection at this location by SNF2h in the presence of ADP-BeF x (Racki et al, 2009).…”

Section: Discussionmentioning

confidence: 99%

A Nucleotide-Driven Switch Regulates Flanking DNA Length Sensing by a Dimeric Chromatin Remodeler

Leonard

Narlikar

2015

Molecular Cell

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SUMMARY The ATP-dependent chromatin assembly factor (ACF) is a dimeric motor that spaces nucleosomes to promote formation of silent chromatin. Two copies of its ATPase subunit SNF2h bind opposite sides of a nucleosome, but how these protomers avoid competition is unknown. SNF2h senses the length of DNA flanking a nucleosome via its HAND-SANT-SLIDE (HSS) domain, yet it is unclear how this interaction enhances remodeling. Using covalently connected SNF2h dimers we show that dimerization accelerates remodeling and that the HSS contributes to communication between protomers. We further identify a nucleotide-dependent conformational change in SNF2h. In one conformation the HSS binds flanking DNA, and in another conformation the HSS engages the nucleosome core. Based on these results, we propose a model in which DNA length sensing and translocation are performed by two distinct conformational states of SNF2h. Such separation of function suggests that these activities could be independently regulated to affect remodeling outcomes.

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“…Interactions between ISW2 and nucleosomes expand on ATP hydrolysis, protecting an additional ~40 bp of nucleosomal DNA, and form a template-committed complex that is resistant to competitor DNA (131). The additional contacts occur between the helicase domain at SHL2 and the HAND domain at SHL6 and may facilitate the entry of DNA into nucleosomes (Figure 4 e ).…”

Section: Operation Of the Helicase Domain Inside Nucleosomesmentioning

confidence: 99%

Regulating the Chromatin Landscape: Structural and Mechanistic Perspectives

Bartholomew

2014

Annu. Rev. Biochem.

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179

170

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A large family of chromatin remodelers that noncovalently modify chromatin are crucial in cell development and differentiation. They are often the targets of cancer, neurological disorders, and other human diseases. These complexes alter nucleosome positioning, higher-order chromatin structure, and nuclear organization. They also assemble chromatin, exchange out histone variants, and disassemble chromatin at defined locations. We review aspects of the structural organization of these complexes, the functional properties of their protein domains, and variation between complexes. We also address the mechanistic details of these complexes in mobilizing nucleosomes and altering chromatin structure. A better understanding of these issues will be vital for further analyses of subunits of these chromatin remodelers, which are being identified as targets in human diseases by NGS (next-generation sequencing).

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Conformational Changes Associated with Template Commitment in ATP-Dependent Chromatin Remodeling by ISW2

Cited by 49 publications

References 28 publications

Human ISWI chromatin-remodeling complexes sample nucleosomes via transient binding reactions and become immobilized at active sites

Human ISWI chromatin-remodeling complexes sample nucleosomes via transient binding reactions and become immobilized at active sites

A Nucleotide-Driven Switch Regulates Flanking DNA Length Sensing by a Dimeric Chromatin Remodeler

Regulating the Chromatin Landscape: Structural and Mechanistic Perspectives

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