Isolation of an activator-dependent, promoter-specific chromatin remodeling factor

Ehrensberger, Andreas H.; Kornberg, Roger D.

doi:10.1073/pnas.1101449108

Cited by 18 publications

(28 citation statements)

References 50 publications

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“…Acid phosphatase induction in phosphate-free medium at 37°C was significantly delayed in the chd1 isw1 double mutant, similar as already reported (25), and even more in a chd1 isw1 isw2 triple mutant, which may speak for a slight role of Isw2 (not followed up further), but reached full final activity levels (Figure 7A). However, concomitant Sth1 td depletion severely compromised PHO5 expression in these mutant backgrounds (Figure 7A).…”

Section: Resultssupporting

confidence: 90%

The RSC chromatin remodeling complex has a crucial role in the complete remodeler set for yeast PHO5 promoter opening

Musladin

Krietenstein

Korber

et al. 2014

Nucleic Acids Research

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Although yeast PHO5 promoter chromatin opening is a founding model for chromatin remodeling, the complete set of involved remodelers remained unknown for a long time. The SWI/SNF and INO80 remodelers cooperate here, but nonessentially, and none of the many tested single or combined remodeler gene mutations could prevent PHO5 promoter opening. RSC, the most abundant and only remodeler essential for viability, was a controversial candidate for the unrecognized remodeling activity but unassessed in vivo. Now we show that remodels the structure of chromatin (RSC) is crucially involved in PHO5 promoter opening. Further, the isw1 chd1 double deletion also delayed chromatin remodeling. Strikingly, combined absence of RSC and Isw1/Chd1 or Snf2 abolished for the first time promoter opening on otherwise sufficient induction in vivo. Together with previous findings, we recognize now a surprisingly complex network of five remodelers (RSC, SWI/SNF, INO80, Isw1 and Chd1) from four subfamilies (SWI/SNF, INO80, ISWI and CHD) as involved in PHO5 promoter chromatin remodeling. This is likely the first described complete remodeler set for a physiological chromatin transition. RSC was hardly involved at the coregulated PHO8 or PHO84 promoters despite cofactor recruitment by the same transactivator and RSC’s presence at all three promoters. Therefore, promoter-specific chromatin rather than transactivators determine remodeler requirements.

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Section: Resultssupporting

confidence: 90%

The RSC chromatin remodeling complex has a crucial role in the complete remodeler set for yeast PHO5 promoter opening

Musladin

Krietenstein

Korber

et al. 2014

Nucleic Acids Research

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“…The inefficiency of competing activities would then have revealed SWI/SNF catalysis of nucleosome disassembly at PHO5 in our strain background. This interpretation is consistent with a recent report that PHO5 expression was marginally compromised in the absence of either Chd1 or Isw1, but abolished in the absence of both chromatin remodelers (25).…”

Section: Discussionsupporting

confidence: 82%

In Vivo Role for the Chromatin-remodeling Enzyme SWI/SNF in the Removal of Promoter Nucleosomes by Disassembly Rather Than Sliding

Brown¹,

Mao²,

Falkovskaia

et al. 2011

Journal of Biological Chemistry

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Background:The enzymatic activities catalyzing disassembly of promoter nucleosomes in vivo are unknown. Results: We show that nucleosomes are lost from activated PHO8 gene and promoter circles, formed in vivo, in an SWI/SNFdependent manner. Conclusion: SWI/SNF plays a role in nucleosome disassembly in vivo. Significance: Our findings are the first demonstration of nucleosome disassembly in vivo dependent on a known chromatinremodeling enzyme.

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“…Indeed, recent studies have demonstrated that in Drosophila, the CHD1 chromodomains, which recognize H3K4me3, are not required for its colocalization to active genes (Morettini et al 2011). Moreover, Kornberg and colleagues (Ehrensberger and Kornberg 2011) have recently found that S. cerevisiae CHD1, whose chromodomains do not recognize H3K4me3, selectively removes nucleosomes at the promoter in vitro and in vivo in an activator-dependent manner. In mammalian cells, the close correlation between localization of Mediator, Chd1, and H3K4me3 and active transcription in mouse ES cells reinforces the notion that the major mechanism for Chd1 localization is PIC assembly.…”

Section: Discussionmentioning

confidence: 99%

“…The CHD1 complex has been shown to associate with the PAF1 elongation complex in Saccharomyces cerevisiae (Warner et al 2007). However, in S. cerevisiae, while CHD1 is capable of remodeling promoter nucleosomes, it does not exhibit preferential binding to H3K4me3 chromatin (Ehrensberger and Kornberg 2011). Thus, in higher eukaryotes, CHD1 is a model H3K4me3 effector used in developmental decisions and elsewhere; its enhancement of gene expression is linked to both transcription and H3K4me3.…”

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confidence: 99%

Mediator coordinates PIC assembly with recruitment of CHD1

Lin¹,

Lehmann²,

Bonora³

et al. 2011

Genes Dev.

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Murine Chd1 (chromodomain helicase DNA-binding protein 1), a chromodomain-containing chromatin remodeling protein, is necessary for embryonic stem (ES) cell pluripotency. Chd1 binds to nucleosomes trimethylated at histone 3 Lys 4 (H3K4me3) near the beginning of active genes but not to bivalent domains also containing H3K27me3. To address the mechanism of this specificity, we reproduced H3K4me3-and CHD1-stimulated gene activation in HeLa extracts. Multidimensional protein identification technology (MuDPIT) and immunoblot analyses of purified preinitiation complexes (PICs) revealed the recruitment of CHD1 to naive chromatin but enhancement on H3K4me3 chromatin. Studies in depleted extracts showed that the Mediator coactivator complex, which controls PIC assembly, is also necessary for CHD1 recruitment. MuDPIT analyses of CHD1-associated proteins support the recruitment data and reveal numerous components of the PIC, including Mediator. In vivo, CHD1 and Mediator are recruited to an inducible gene, and genome-wide binding of the two proteins correlates well with active gene transcription in mouse ES cells. Finally, coimmunoprecipitation of CHD1 and Mediator from cell extracts can be ablated by shRNA knockdown of a specific Mediator subunit. Our data support a model in which the Mediator coordinates PIC assembly along with the recruitment of CHD1. The combined action of the PIC and H3K4me3 provides specificity in targeting CHD1 to active genes.

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Isolation of an activator-dependent, promoter-specific chromatin remodeling factor

Cited by 18 publications

References 50 publications

The RSC chromatin remodeling complex has a crucial role in the complete remodeler set for yeast PHO5 promoter opening

The RSC chromatin remodeling complex has a crucial role in the complete remodeler set for yeast PHO5 promoter opening

In Vivo Role for the Chromatin-remodeling Enzyme SWI/SNF in the Removal of Promoter Nucleosomes by Disassembly Rather Than Sliding

Mediator coordinates PIC assembly with recruitment of CHD1

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