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author:("flaps, Andrew")
1.  Mechanisms for ATP-dependent chromatin remodelling: The means to the end 
The FEBS journal  2011;278(19):3579-3595.
Summary
Chromatin remodelling is the ATP-dependent change in nucleosome organisation driven by Snf2 family ATPases. The biochemistry of this process depends on the behaviours of ATP dependent motor proteins and their dynamic nucleosome substrates, which brings significant technical and conceptual challenges. Steady progress has been made in characterizing the polypeptides that these enzymes are comprised of. Divergence in the sequences of different subfamilies of Snf2 related proteins suggests that the motors are adapted for different functions. Recently structural insights have suggested that the Snf2 ATPase acts as a context-sensitive DNA translocase. This may have arisen as a means to enable efficient access to DNA in the high density of the eukaryotic nucleus. How the enzymes engage nucleosomes and how the network of non-covalent interactions within the nucleosome respond to the force applied remains unclear, and it remains prudent to recognise the potential for both DNA distortions and dynamics within the underlying histone octamer structure.
doi:10.1111/j.1742-4658.2011.08281.x
PMCID: PMC4162296  PMID: 21810178
2.  Nucleosomes can invade DNA territories occupied by their neighbors 
Nucleosomes are the fundamental subunits of eukaryotic chromatin. They are not static entities, but can undergo a number of dynamic transitions including spontaneous repositioning along DNA. Since nucleosomes are spaced close together within genomes it is likely that on occasion they approach each other and or collide. Here we have used a dinucleosomal model system to show that the 147bp DNA territories of two nucleosomes can overlap extensively. In the situation of an overlap by 44 bp or 54 bp one histone dimer is lost and the resulting complex can condense to form a compact single particle. We propose a pathway in which adjacent nucleosomes promote DNA unraveling as they approach each other and that this permits their 147bp territories to overlap. These may represent early steps in a pathway for nucleosome removal via collision.
doi:10.1038/nsmb.1551
PMCID: PMC2675935  PMID: 19182801
3.  Histone Modifications Influence the Action of Snf2 Family Remodelling Enzymes by Different Mechanisms 
Journal of Molecular Biology  2007;374(3):563-579.
Alteration of chromatin structure by chromatin modifying and remodelling activities is a key stage in the regulation of many nuclear processes. These activities are frequently interlinked, and many chromatin remodelling enzymes contain motifs that recognise modified histones. Here we adopt a peptide ligation strategy to generate specifically modified chromatin templates and used these to study the interaction of the Chd1, Isw2 and RSC remodelling complexes with differentially acetylated nucleosomes. Specific patterns of histone acetylation are found to alter the rate of chromatin remodelling in different ways. For example, histone H3 lysine 14 acetylation acts to increase recruitment of the RSC complex to nucleosomes. However, histone H4 tetra-acetylation alters the spectrum of remodelled products generated by increasing octamer transfer in trans. In contrast, histone H4 tetra-acetylation was also found to reduce the activity of the Chd1 and Isw2 remodelling enzymes by reducing catalytic turnover without affecting recruitment. These observations illustrate a range of different means by which modifications to histones can influence the action of remodelling enzymes.
doi:10.1016/j.jmb.2007.09.059
PMCID: PMC2279226  PMID: 17949749
Histone; Acetylation; Snf2; Nucleosome; Chromatin
4.  Histone Tails and the H3 αN Helix Regulate Nucleosome Mobility and Stability▿  
Molecular and Cellular Biology  2007;27(11):4037-4048.
Nucleosomes fulfill the apparently conflicting roles of compacting DNA within eukaryotic genomes while permitting access to regulatory factors. Central to this is their ability to stably associate with DNA while retaining the ability to undergo rearrangements that increase access to the underlying DNA. Here, we have studied different aspects of nucleosome dynamics including nucleosome sliding, histone dimer exchange, and DNA wrapping within nucleosomes. We find that alterations to histone proteins, especially the histone tails and vicinity of the histone H3 αN helix, can affect these processes differently, suggesting that they are mechanistically distinct. This raises the possibility that modifications to histone proteins may provide a means of fine-tuning specific aspects of the dynamic properties of nucleosomes to the context in which they are located.
doi:10.1128/MCB.02229-06
PMCID: PMC1900026  PMID: 17387148
5.  ANALYSIS OF NUCLEOSOME REPOSITIONING BY YEAST ISWI AND CHD1 CHROMATIN REMODELLING COMPLEXES 
The Journal of biological chemistry  2006;281(24):16279-16288.
ISWI proteins form the catalytic core of a subset of ATP-dependent chromatin remodelling activities in eukaryotes from yeast to man. Many of these complexes have been found to reposition nucleosomes, but with different directionalities. We find that the yeast Isw1a, Isw2 and Chd1 enzymes preferentially move nucleosomes towards more central locations on short DNA fragments whereas Isw1b does not. Importantly, the inherent positioning properties of the DNA play an important role in determining where nucleosomes are relocated to by all of these enzymes. However, a key difference is that the Isw1a, Isw2 and Chd1 enzymes are unable to move nucleosomes to positions closer than 15 bp from a DNA end whereas Isw1b can. We also find that there is a correlation between the inability of enzymes to move nucleosomes close to DNA ends and the preferential binding to nucleosomes bearing linker DNA. These observations suggest that the accessibility of linker DNA together with the positioning properties of the underlying DNA play important roles in determining the outcome of remodelling by these enzymes.
doi:10.1074/jbc.M600682200
PMCID: PMC1764501  PMID: 16606615
6.  Snf2 family ATPases and DExx box helicases: differences and unifying concepts from high-resolution crystal structures 
Nucleic Acids Research  2006;34(15):4160-4167.
Proteins with sequence similarity to the yeast Snf2 protein form a large family of ATPases that act to alter the structure of a diverse range of DNA–protein structures including chromatin. Snf2 family enzymes are related in sequence to DExx box helicases, yet they do not possess helicase activity. Recent biochemical and structural studies suggest that the mechanism by which these enzymes act involves ATP-dependent translocation on DNA. Crystal structures suggest that these enzymes travel along the minor groove, a process that can generate the torque or energy in remodelling processes. We review the recent structural and biochemical findings which suggest a common mechanistic basis underlies the action of many of both Snf2 family and DExx box helicases.
doi:10.1093/nar/gkl540
PMCID: PMC1616948  PMID: 16935875
7.  Identification of multiple distinct Snf2 subfamilies with conserved structural motifs 
Nucleic Acids Research  2006;34(10):2887-2905.
The Snf2 family of helicase-related proteins includes the catalytic subunits of ATP-dependent chromatin remodelling complexes found in all eukaryotes. These act to regulate the structure and dynamic properties of chromatin and so influence a broad range of nuclear processes. We have exploited progress in genome sequencing to assemble a comprehensive catalogue of over 1300 Snf2 family members. Multiple sequence alignment of the helicase-related regions enables 24 distinct subfamilies to be identified, a considerable expansion over earlier surveys. Where information is known, there is a good correlation between biological or biochemical function and these assignments, suggesting Snf2 family motor domains are tuned for specific tasks. Scanning of complete genomes reveals all eukaryotes contain members of multiple subfamilies, whereas they are less common and not ubiquitous in eubacteria or archaea. The large sample of Snf2 proteins enables additional distinguishing conserved sequence blocks within the helicase-like motor to be identified. The establishment of a phylogeny for Snf2 proteins provides an opportunity to make informed assignments of function, and the identification of conserved motifs provides a framework for understanding the mechanisms by which these proteins function.
doi:10.1093/nar/gkl295
PMCID: PMC1474054  PMID: 16738128
8.  Dynamic Properties of Nucleosomes during Thermal and ATP-Driven Mobilization 
Molecular and Cellular Biology  2003;23(21):7767-7779.
The fundamental subunit of chromatin, the nucleosome, is not a static entity but can move along DNA via either thermal or enzyme-driven movements. Here we have monitored the movements of nucleosomes following deposition at well-defined locations on mouse mammary tumor virus promoter DNA. We found that the sites to which nucleosomes are deposited during chromatin assembly differ from those favored during thermal equilibration. Taking advantage of this, we were able to track the movement of nucleosomes over 156 bp and found that this proceeds via intermediate positions spaced between 46 and 62 bp. The remodeling enzyme ISWI was found to direct the movement of nucleosomes to sites related to those observed during thermal mobilization. In contrast, nucleosome mobilization driven by the SWI/SNF and RSC complexes were found to drive nucleosomes towards sites up to 51 bp beyond DNA ends, with little respect for the sites favored during thermal repositioning. The dynamic properties of nucleosomes we describe are likely to influence their role in gene regulation.
doi:10.1128/MCB.23.21.7767-7779.2003
PMCID: PMC207611  PMID: 14560021
9.  Evidence for DNA Translocation by the ISWI Chromatin-Remodeling Enzyme 
Molecular and Cellular Biology  2003;23(6):1935-1945.
The ISWI proteins form the catalytic core of a subset of ATP-dependent chromatin-remodeling activities. Here, we studied the interaction of the ISWI protein with nucleosomal substrates. We found that the ability of nucleic acids to bind and stimulate the ATPase activity of ISWI depends on length. We also found that ISWI is able to displace triplex-forming oligonucleotides efficiently when they are introduced at sites close to a nucleosome but successively less efficiently 30 to 60 bp from its edge. The ability of ISWI to direct triplex displacement was specifically impeded by the introduction of 5- or 10-bp gaps in the 3′-5′ strand between the triplex and the nucleosome. In combination, these observations suggest that ISWI is a 3′-5′-strand-specific, ATP-dependent DNA translocase that may be capable of forcing DNA over the surface of nucleosomes.
doi:10.1128/MCB.23.6.1935-1945.2003
PMCID: PMC149479  PMID: 12612068

Results 1-9 (9)