van Vugt, J.J., Ranes, M., Campsteijn, C. & Logie, C. The ins and outs of ATP-dependent chromatin remodeling in budding yeast: biophysical and proteomic perspectives. Biochim. Biophys. Acta 1769, 153-171

Radboud University Nijmegen, Nymegen, Gelderland, Netherlands
Biochimica et Biophysica Acta (Impact Factor: 4.66). 03/2007; 1769(3):153-171. DOI: 10.1016/j.bbaexp.2007.01.013


ATP-dependent chromatin remodeling is performed by multi-subunit protein complexes. Over the last years, the identity of these factors has been unveiled in yeast and many parallels have been drawn with animal and plant systems, indicating that sophisticated chromatin transactions evolved prior to their divergence. Here we review current knowledge pertaining to the molecular mode of action of ATP-dependent chromatin remodeling, from single molecule studies to genome-wide genetic and proteomic studies. We focus on the budding yeast versions of SWI/SNF, RSC, DDM1, ISWI, CHD1, INO80 and SWR1.

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Available from: Joke van Vugt
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    • "RSC is also involved in DNA repair [6]. Two different isoforms of RSC that are composed of up to 17 proteins exist in S. cerevisiae [7] [8]: the Rsc1 complex is comprised of Rsc1p, Rsc3p, Rsc4p, Rsc6p, Rsc8p, Rsc9p, Rsc30p, Rsc58p, Sfh1p, Sth1p, Rtt102p, Npl6p, Ldb7p, Htl1p, Arp7p, Arp9p as well as actin. Rsc3p and Rsc30p are underrepresented in the Rsc2 complex, and Rsc1p is replaced by Rsc2p [9]. "
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    ABSTRACT: Affinity isolation has been an essential technique for molecular studies of cellular assemblies, such as the switch/sucrose non-fermentable (SWI/SNF) family of ATP-dependent chromatin remodeling complexes. However, even biochemically pure isolates can contain heterogeneous mixtures of complexes and their components. In particular, purification strategies that rely on affinity tags fused to only one component of a complex may be susceptible to this phenomenon. This study demonstrates that fusing purification tags to two different proteins enables the isolation of intact complexes of remodels the structure of chromatin (RSC). A Protein A tag was fused to one of the RSC proteins and a Twin-Strep tag to another protein of the complex. By mass spectrometry, we demonstrate the enrichment of the RSC complexes. The complexes had an apparent Svedberg value of about 20S, as shown by glycerol gradient ultracentrifugation. Additionally, purified complexes were demonstrated to be functional. Electron microscopy and single-particle analyses revealed a conformational rearrangement of RSC upon interaction with acetylated histone H3 peptides. This purification method is useful to purify functionally active, structurally well-defined macromolecular assemblies. Copyright © 2014. Published by Elsevier B.V.
    Full-text · Article · Dec 2014 · Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics
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    • "Two major classes include hSWI/ SNF-A or BAF (BRG1-associated Factor) complex and hSWI/SNF- B or PBAF complex. The two classes of complexes are distinguished by the presence of specific subunits [Martens and Winston, 2003; van Vugt et al., 2007]. Additional complexes containing mixtures of components of SWI/SNF and HDAC1 complexes have also been identified (See Fig. 2) [Martens and Winston, 2003]. "
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    ABSTRACT: Schwannomatosis is the third major form of neurofibromatosis and is characterized by the development of multiple schwannomas in the absence of bilateral vestibular schwannomas. The 2011 Schwannomatosis Update was organized by the Children's Tumor Foundation ( and held in Los Angeles, CA, from June 5-8, 2011. This article summarizes the highlights presented at the Conference and represents the "state-of-the-field" in 2011. Genetic studies indicate that constitutional mutations in the SMARCB1 tumor suppressor gene occur in 40-50% of familial cases and in 8-10% of sporadic cases of schwannomatosis. Tumorigenesis is thought to occur through a four-hit, three-step model, beginning with a germline mutation in SMARCB1 (hit 1), followed by loss of a portion of chromosome 22 that contains the second SMARCB1 allele and one NF2 allele (hits 2 and 3), followed by mutation of the remaining wild-type NF2 allele (hit 4). Insights from research on HIV and pediatric rhabdoid tumors have shed light on potential molecular pathways that are dysregulated in schwannomatosis-related schwannomas. Mouse models of schwannomatosis have been developed and promise to further expand our understanding of tumorigenesis and the tumor microenvironment. Clinical reports have described the occurrence of intracranial meningiomas in schwannomatosis patients and in families with germline SMARCB1 mutations. The authors propose updated diagnostic criteria to incorporate new clinical and genetic findings since 2005. In the next 5 years, the authors expect that advances in basic research in the pathogenesis of schwannomatosis will lead toward clinical investigations of potential drug therapies. © 2013 Wiley Periodicals, Inc.
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    • "Nucleosomes can form on virtually any DNA sequence, though some are more or less favoured. Histones are assembled onto chromosomal DNA by histone chaperones [3] [4] [5] [6], often in conjunction with ATPases [7] [8] [9] [10] [11]. Once assembled, nucleosomes can be moved enzymatically to new locations along the DNA [12] [13] [14] [15]. "
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    ABSTRACT: Histones are highly basic, relatively small proteins that complex with DNA to form higher order structures that underlie chromosome topology. Of the four core histones H2A, H2B, H3 and H4, it is H3 that is most heavily modified at the post-translational level. The human genome harbours 16 annotated bona fide histone H3 genes which code for four H3 protein variants. In 2010, two novel histone H3.3 protein variants were reported, carrying over twenty amino acid substitutions. Nevertheless, they appear to be incorporated into chromatin. Interestingly, these new H3 genes are located on human chromosome 5 in a repetitive region that harbours an additional five H3 pseudogenes, but no other core histone ORFs. In addition, a human-specific novel putative histone H3.3 variant located at 12p11.21 was reported in 2011. These developments raised the question as to how many more human histone H3 ORFs there may be. Using homology searches, we detected 41 histone H3 pseudogenes in the current human genome assembly. The large majority are derived from the H3.3 gene H3F3A, and three of those may code for yet more histone H3.3 protein variants. We also identified one extra intact H3.2-type variant ORF in the vicinity of the canonical HIST2 gene cluster at chromosome 1p21.2. RNA polymerase II occupancy data revealed heterogeneity in H3 gene expression in human cell lines. None of the novel H3 genes were significantly occupied by RNA polymerase II in the data sets at hand, however. We discuss the implications of these recent developments.
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