ACF1 improves the effectiveness of nucleosome mobilization by ISWI through PHD–histone contacts

Eberharter, Anton; Vetter, I.R.; Ferreira, Roger; Becker, Peter B.

doi:10.1038/sj.emboj.7600382

Cited by 107 publications

(106 citation statements)

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“…PHD fingers are found in multiple complexes that regulate chromatin structure; however, the function of the majority of these domains is unknown. The PHD fingers of the p300 histone acetyltransferase and ACF1, a subunit of an ATP-dependent nucleosome remodeling complex, are required for these proteins to bind histones (12,54), but whether this binding is dependent on the methylation state of the histones was not investigated. However, the fact that the binding of the ACF1 PHD fingers to histones was not dependent on the presence of the histone tails argues against this possibility for ACF1 (12).…”

Section: Discussionmentioning

confidence: 99%

“…Members of the ING family contain a PHD finger domain within their carboxyl termini (21). This zinc finger-like motif is found in various proteins involved in chromatin-mediated gene regulation (1), and several studies have implicated PHD fingers in mediating the interaction of chromatin-modifying factors with histones (12,54). Indeed, the Yng2p PHD finger is required for full activation of NuA4-dependent genes, suggesting that this motif is required for some aspect of HAT complex function (46).…”

Section: Yng1p Interacts With the Histone H3 Tail In Vivomentioning

confidence: 99%

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The Yng1p Plant Homeodomain Finger Is a Methyl-Histone Binding Module That Recognizes Lysine 4-Methylated Histone H3

Martin¹,

Baetz

Shi

et al. 2006

Molecular and Cellular Biology

145

114

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The ING (inhibitor of growth) protein family includes a group of homologous nuclear proteins that share a highly conserved plant homeodomain (PHD) finger domain at their carboxyl termini. Members of this family are found in multiprotein complexes that posttranslationally modify histones, suggesting that these proteins serve a general role in permitting various enzymatic activities to interact with nucleosomes. There are three members of the ING family in Saccharomyces cerevisiae: Yng1p, Yng2p, and Pho23p. Yng1p is a component of the NuA3 histone acetyltransferase complex and is required for the interaction of NuA3 with chromatin. To gain insight into the function of the ING proteins, we made use of a genetic strategy to identify genes required for the binding of Yng1p to histones. Using the toxicity of YNG1 overexpression as a tool, we showed that Yng1p interacts with the amino-terminal tail of histone H3 and that this interaction can be disrupted by loss of lysine 4 methylation within this tail. Additionally, we mapped the region of Yng1p required for overexpression of toxicity to the PHD finger, showed that this region capable of binding lysine 4-methylated histone H3 in vitro, and demonstrated that mutations of the PHD finger that abolish binding in vitro are no longer toxic in vivo. These results identify a novel function for the Yng1p PHD finger in promoting stabilization of the NuA3 complex at chromatin through recognition of histone H3 lysine 4 methylation.Chromatin structure can be regulated by the addition of posttranslational modifications to histones, including acetylation, methylation, phosphorylation, and ubiquitination. These modifications are thought to function by creating docking sites for factors which alter chromatin structure (27,58). Consistent with this, several protein motifs have been identified that mediate the selective interaction of transcription-regulating complexes with specific histone modifications. The first such identified motif is the bromodomain, which preferentially interacts with acetylated histones (7,10,24,49,50,65). Bromodomains are found in a number of protein complexes, including components of the basal transcription machinery and chromatin remodeling complexes (20, 41), which may explain, in part, how histone acetylation can facilitate transcription. Bromodomains are also found in a number of histone methyltransferases, suggesting that histone acetylation can mediate histone methylation (6). The ability of one histone modification to recruit another histone-modifying enzyme is a common recurring theme in chromatin research.A second motif which has been shown to bind modified histones is the chromodomain, which preferentially interacts with methylated lysines (19,52). Chromodomains are found in proteins involved in both the activation and silencing of transcription, consistent with the role of histone methylation in both events (31). Similar to bromodomains, chromodomains are found in chromatin remodeling complexes, histone acetyltransferases, and histone methyltransfer...

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Section: Discussionmentioning

confidence: 99%

Section: Yng1p Interacts With the Histone H3 Tail In Vivomentioning

confidence: 99%

The Yng1p Plant Homeodomain Finger Is a Methyl-Histone Binding Module That Recognizes Lysine 4-Methylated Histone H3

Martin¹,

Baetz

Shi

et al. 2006

Molecular and Cellular Biology

145

114

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“…Acf1 contains WAC (WSTF, Acf1, cbp146p), WAKZ (WSTF, Acf1, KIAA0314, ZK783.4), DDT (DNA binding homeobox and Different Transcription factors), BAZ , two PHD (Plant homeodomain) fingers and a bromodomain [101]. The two PHD fingers were found to increase the efficiency of nucleosome mobilization by ACF in Drosophila [102]. Isw1p and Isw2p of S.cerevisiae share the same domain organization as dISWI except that the AID domain is absent in the yeast counterparts.…”

Section: Iswi Familymentioning

confidence: 99%

Mechanisms of ATP dependent chromatin remodeling

Gangaraju

Bartholomew

2007

Mutation Research/Fundamental and Molecular Mechanisms of Mutag

128

159

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The inter-relationship between DNA repair and ATP dependent chromatin remodeling has begun to become very apparent with recent discoveries. ATP dependent remodeling complexes mobilize nucleosomes along DNA, promote the exchange of histones, or completely displace nucleosomes from DNA. These remodeling complexes are often categorized based on the domain organization of their catalytic subunit. The biochemical properties and structural information of several of these remodeling complexes are reviewed. The different models for how these complexes are able to mobilize nucleosomes and alter nucleosome structure are presented incorporating several recent findings. Finally the role of histone tails and their respective modifications in ATP-dependent remodeling are discussed.

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“…ACF docks solidly to the nucleosome via PHD fingers in the core histones. 133 Deletion of PHD modules abolishes ACF subunit Acf1-directed nucleosome repressive mobilization. 133 ACF is a member of the SF2 family of ISWI-class of ATPases, which includes DExx-box proteins such as helicases and nucleic acid translocases, SNF2 h and CHRAC.…”

mentioning

confidence: 99%

“…133 Deletion of PHD modules abolishes ACF subunit Acf1-directed nucleosome repressive mobilization. 133 ACF is a member of the SF2 family of ISWI-class of ATPases, which includes DExx-box proteins such as helicases and nucleic acid translocases, SNF2 h and CHRAC. Acf1 is involved in the strategic deposition of histones in periodic nucleosome arrangement around methylated CpG DNA targeted for silencing and is assisted by the chaperones NAP-1 and CAF-1.…”

mentioning

confidence: 99%