Nucleosome sliding mechanisms: new twists in a looped history

Mueller-Planitz, Felix; Klinker, Henrike; Becker, Peter B.

doi:10.1038/nsmb.2648

Cited by 96 publications

(104 citation statements)

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“…In contrast, the 720-kDa band yielded all components except for CHD4. The same conclusion is reached when the purified complex (bound to fluorescein-labeled FOG1 (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)) is subjected to sucrose density gradient ultracentrifugation; fluorescent signals corresponding to NuDe and NuRD were observed at two distinct positions in the gradient (Fig. 4A).…”

Section: Resultsmentioning

confidence: 58%

“…ATP-dependent chromatin remodeling enzymes solve this problem by using ATP-derived energy to alter the positions, occupancy and composition of nucleosomes. All remodelers possess a highly related ATPase motor domain from the helicase family and are classified into four subfamilies (INO80, ISWI, SWR1, and CHD) based on sequence similarity (1). Each subfamily is represented in nearly all eukaryotes, suggesting that they catalyze different remodeling events.…”

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confidence: 99%

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CHD4 Is a Peripheral Component of the Nucleosome Remodeling and Deacetylase Complex

Low

Webb

Silva

et al. 2016

Journal of Biological Chemistry

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Chromatin remodeling enzymes act to dynamically regulate gene accessibility. In many cases, these enzymes function as large multicomponent complexes that in general comprise a central ATP-dependent Snf2 family helicase that is decorated with a variable number of regulatory subunits. The nucleosome remodeling and deacetylase (NuRD) complex, which is essential for normal development in higher organisms, is one such macromolecular machine. The NuRD complex comprises ϳ10 subunits, including the histone deacetylases 1 and 2 (HDAC1 and HDAC2), and is defined by the presence of a CHD family remodeling enzyme, most commonly CHD4 (chromodomain helicase DNA-binding protein 4). The existing paradigm holds that CHD4 acts as the central hub upon which the complex is built. We show here that this paradigm does not, in fact, hold and that CHD4 is a peripheral component of the NuRD complex. A complex lacking CHD4 that has HDAC activity can exist as a stable species. The addition of recombinant CHD4 to this nucleosome deacetylase complex reconstitutes a NuRD complex with nucleosome remodeling activity. These data contribute to our understanding of the architecture of the NuRD complex.Nucleosomes effectively act as a roadblock to all aspects of genome biology. ATP-dependent chromatin remodeling enzymes solve this problem by using ATP-derived energy to alter the positions, occupancy and composition of nucleosomes. All remodelers possess a highly related ATPase motor domain from the helicase family and are classified into four subfamilies (INO80, ISWI, SWR1, and CHD) based on sequence similarity (1). Each subfamily is represented in nearly all eukaryotes, suggesting that they catalyze different remodeling events. For example, ISWI proteins reposition (or slide) nucleosomes to create regularly spaced arrays; this periodic organization is a key characteristic of DNA at the start of genes (2). SWR1 and INO80 enzymes have opposing roles in histone variant dynamics; the former incorporates these histone variants (e.g. H2A.Z), whereas the latter removes them. These variants set up specific chromatin structures that modulate transcription and replication, although the roles of many variants are still under debate (3). Fundamentally, these remodeling enzymes all alter the accessibility of DNA to other DNA-binding factors and thereby broadly underpin genome biology.Remodelers frequently act in the context of large multisubunit complexes, and in general, the "mixing and matching" of complex composition can generate complexes with varying activities; the human ISWI protein Snf2h for instance has been identified in six distinct complexes (4). Likewise, the accessory subunits can also modulate remodeler activity. For example, the paralogous methyl-CpG-binding domain proteins 2 and 3 (MBD2 and MBD3) subunits of the nucleosome remodeling and deacetylase (NuRD) 6 complex are mutually exclusive (5); MBD2 recognizes 5-methylcytosine-modified DNA, whereas MBD3 instead binds to 5-hydroxymethylated DNA (6, 7). Unsurprisingly, it has been observed tha...

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Section: Resultsmentioning

confidence: 58%

mentioning

confidence: 99%

CHD4 Is a Peripheral Component of the Nucleosome Remodeling and Deacetylase Complex

Low

Webb

Silva

et al. 2016

Journal of Biological Chemistry

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“…. Second, ATP-dependent chromatin remodelers, such as ISWI and SWI/SNF, also disrupt local DNA-histone contacts, creating DNA loops or bulges on nucleosomes during DNA translocation (Mueller-Planitz et al 2013;Bartholomew 2014). Such disruption of local DNA-histone contacts may promote the exposure of the HBR, which triggers the FACT invasion into nucleosomes.…”

Section: Discussionmentioning

confidence: 99%

Integrated molecular mechanism directing nucleosome reorganization by human FACT

et al. 2016

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Facilitates chromatin transcription (FACT) plays essential roles in chromatin remodeling during DNA transcription, replication, and repair. Our structural and biochemical studies of human FACT-histone interactions present precise views of nucleosome reorganization, conducted by the FACT-SPT16 (suppressor of Ty 16) Mid domain and its adjacent acidic AID segment. AID accesses the H2B N-terminal basic region exposed by partial unwrapping of the nucleosomal DNA, thereby triggering the invasion of FACT into the nucleosome. The crystal structure of the Mid domain complexed with an H3-H4 tetramer exhibits two separate contact sites; the Mid domain forms a novel intermolecular β structure with H4. At the other site, the Mid-H2A steric collision on the H2A-docking surface of the H3-H4 tetramer within the nucleosome induces H2A-H2B displacement. This integrated mechanism results in disrupting the H3 αN helix, which is essential for retaining the nucleosomal DNA ends, and hence facilitates DNA stripping from histone.

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“…Chromatin remodelers lack helicase activity (86), but they share the ATP-dependent DNA translocation activity of helicases (27,(87)(88)(89)(90). Furthermore, nucleosome repositioning activity is underpinned by DNA translocation in most models (85,(91)(92)(93)(94)(95). Qualitative demonstrations of DNA translocation by chromatin remodelers, have recently been extended by quantitative determinations of the kinetic mechanism of translocation (87,88,96,97).…”

Section: Dna Translocation By Chromatin Remodeling Enzymesmentioning

confidence: 99%

“…Molecular motors called chromatin remodelers can relieve the inhibition of these processes by sliding or disassembling the nucleosomes (7-9) and thereby serve an essential role in the regulation of gene expression (83). Based upon their highly conserved ATPase domain chromatin remodelers are classified as part of a large Snf2 family of proteins, which in turn is part of the helicase superfamily SF2 (Figure 4) (84,85). Chromatin remodelers lack helicase activity (86), but they share the ATP-dependent DNA translocation activity of helicases (27,(87)(88)(89)(90).…”

Section: Dna Translocation By Chromatin Remodeling Enzymesmentioning

confidence: 99%

All motors have to decide is what to do with the DNA that is given them

Briggs

Fischer

2014

Biomolecular Concepts

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DNA translocases are a diverse group of molecular motors responsible for a wide variety of cellular functions. The goal of this review is to identify common aspects in the mechanisms for how these enzymes couple the binding and hydrolysis of ATP to their movement along DNA. Not surprisingly, the shared structural components contained within the catalytic domains of several of these motors appear to give rise to common aspects of DNA translocation. Perhaps more interesting, however, are the differences between the families of translocases and the potential associated implications both for the functions of the members of these families and for the evolution of these families. However, as there are few translocases for which complete characterizations of the mechanisms of DNA binding, DNA translocation, and DNA-stimulated ATPase have been completed, it is difficult to form many inferences. We therefore hope that this review motivates the necessary further experimentation required for broader comparisons and conclusions.

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Nucleosome sliding mechanisms: new twists in a looped history

Cited by 96 publications

References 96 publications

CHD4 Is a Peripheral Component of the Nucleosome Remodeling and Deacetylase Complex

CHD4 Is a Peripheral Component of the Nucleosome Remodeling and Deacetylase Complex

Integrated molecular mechanism directing nucleosome reorganization by human FACT

All motors have to decide is what to do with the DNA that is given them

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