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Results for “ATP dependent chromatin remodeling”

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At least 19 recordsLinked to original sources

PubMed2000

Generation of superhelical torsion by ATP-dependent chromatin remodeling activities.

ATP-dependent chromatin remodeling activities participate in the alteration of chromatin structure during gene regulation. All have DNA- or chromatin-stimulated ATPase activity and many can alter the structure of chromatin; however, the means by which they do this have remained unclear. Here we describe a novel activity for ATP-dependent chromatin remodeling activities, the ability to generate unconstrained negative superhelical torsion in DNA and chromatin. We find that the ability to distort DNA is shared by the yeast SWI/SNF complex, Xenopus Mi-2 complex, recombinant ISWI, and recombinant BRG1, suggesting that the generation of superhelical torsion represents a primary biomechanical activity shared by all Snf2p-related ATPase motors. The generation of superhelical torque provides a potent means by which ATP-dependent chromatin remodeling activities can manipulate chromatin structure.

Adenosine Triphosphate↗

PubMed2003

Histone H2A/H2B dimer exchange by ATP-dependent chromatin remodeling activities.

ATP-dependent chromatin remodeling activities function to manipulate chromatin structure during gene regulation. One of the ways in which they do this is by altering the positions of nucleosomes along DNA. Here we provide support for the ability of these complexes to move nucleosomes into positions in which DNA is unraveled from one edge. This is expected to result in the loss of histone-DNA contacts that are important for retention of one H2A/H2B dimer within the nucleosome. Consistent with this we find that several chromatin remodeling complexes are capable of catalyzing the exchange of H2A/H2B dimers between chromatin fragments in an ATP-dependent reaction. This provides eukaryotes with additional means by which they may manipulate chromatin structure.

Adenosine Triphosphatases↗

PubMed2001

ATP-dependent chromatin remodeling factors: nucleosome shufflers with many missions.

This review addresses recent developments in the field of ATP-dependent chromatin remodeling factors. These factors use the energy of ATP hydrolysis to introduce superhelical torsion into DNA, which suggests a common mechanistic basis of action. Chromatin remodeling factors function both in transcriptional activation and repression, but they may have roles outside of transcriptional regulation such as DNA repair. A study of the nucleosome dependent ATPase ISWI in yeast illustrates the involvement of ATP-dependent chromatin remodeling in transcriptional repression by setting up inaccessible chromatin structures at promoters. However, factors such as ISWI are also involved in the restructuring of large chromatin domains and even whole chromosomes. Transcriptional regulation by ATP-dependent chromatin remodeling factors occurs in concert with histone modifying enzymes such as histone acetyltransferases and histone deacetylases: In yeast, SWI/SNF targeting is a requirement for histone acetyltransferases activity at promoters that are active at late stages of mitosis, when the chromatin is still condensed. This demonstrates that ATP-dependent remodeling factors facilitate covalent histone modifications. However, they are also regulated by histone modifications and in some circumstances they function in parallel with histone modifications towards the same goal.

Adenosine Triphosphatases↗

PubMed2004

Mechanisms for ATP-dependent chromatin remodelling: farewell to the tuna-can octamer?

ATP-dependent chromatin remodelling enzymes act to alter chromatin structure during gene regulation. Studies of the ATPase motors that drive these enzymes support the notion that they function as ATP-dependent DNA translocases with limited processivity. The action of these enzymes on nucleosomes results in the alteration of nucleosome positioning and structure. Recent studies have shown that ATP-dependent chromatin remodelling can also either remove or exchange histone dimers between nucleosomes. This provides a new means by which the incorporation of histone variants can be directed. Additional observations support roles for ATP-dependent remodelling enzymes throughout the transcription cycle.

Adenosine Triphosphatases↗

PubMed2004

INO80 and gamma-H2AX interaction links ATP-dependent chromatin remodeling to DNA damage repair.

While the role of ATP-dependent chromatin remodeling in transcription is well established, a link between chromatin remodeling and DNA repair has remained elusive. We have found that the evolutionarily conserved INO80 chromatin remodeling complex directly participates in the repair of a double-strand break (DSB) in yeast. The INO80 complex is recruited to a HO endonuclease-induced DSB through a specific interaction with the DNA damage-induced phosphorylated histone H2A (gamma-H2AX). This interaction requires Nhp10, an HMG-like subunit of the INO80 complex. The loss of Nhp10 or gamma-H2AX results in reduced INO80 recruitment to the DSB. Finally, components of the INO80 complex show synthetic genetic interactions with the RAD52 DNA repair pathway, the main pathway for DSB repair in yeast. Our findings reveal a new role of ATP-dependent chromatin remodeling in nuclear processes and suggest that an ATP-dependent chromatin remodeling complex can read a DNA repair histone code.

Adenosine Triphosphate↗

PubMed2002

Phosphorylation of linker histones regulates ATP-dependent chromatin remodeling enzymes.

Members of the ATP-dependent family of chromatin remodeling enzymes play key roles in the regulation of transcription, development, DNA repair and cell cycle control. We find that the remodeling activities of the ySWI/SNF, hSWI/SNF, xMi-2 and xACF complexes are nearly abolished by incorporation of linker histones into nucleosomal array substrates. Much of this inhibition is independent of linker histone-induced folding of the arrays. We also find that phosphorylation of the linker histone by Cdc2/Cyclin B kinase can rescue remodeling by ySWI/SNF. These results suggest that linker histones exert a global, genome-wide control over remodeling activities, implicating a new, obligatory coupling between linker histone kinases and ATP-dependent remodeling enzymes.

APOBEC-1 Deaminase↗

PubMed2026

ATP-Dependent Chromatin Remodelers in Prostate Cancer Progression and Therapeutic Resistance.

ATP-dependent chromatin remodelers (ACRs) have emerged as central determinants of prostate cancer (PCa) progression and therapy resistance. Organized into four mechanistically distinct families (SWI/SNF, ISWI, CHD, and INO80/SWR), ACRs govern nucleosome positioning genome-wide and thereby occupy a central position in the epigenomic regulatory landscape that dictates where and when transcription factors, including the androgen receptor (AR), can engage chromatin. This review discusses ACR dysregulation in PCa through both mutational and non-mutational mechanisms. These are illustrated by discussing how the functional consequences are highly context-dependent, varying with disease stage, prior treatment exposure, and tumor ancestry. Loss of the tumor suppressors RB1, TP53, and PTEN each generates specific ACR dependencies that are potentially therapeutically exploitable, including synthetic lethal relationships between PTEN deficiency and SWI/SNF ATPase activity. Across the spectrum of AR signaling states, from hormone-sensitive disease through therapy-resistant neuroendocrine and double-negative PCa subtypes, ACR complex composition and genomic targeting are continuously reprogrammed to enable and sustain lineage plasticity and endocrine therapy escape. Therapeutic strategies targeting SWI/SNF, ISWI, and INO80/SWR complexes are at varying stages of preclinical and clinical development and are attractive novel avenues to target therapy resistant PCa.

ATP dependent chromatin remodeling↗

PubMed2001

ATP-dependent chromatin remodeling activities.

Genetic and biochemical approaches have indicated that the packaging of DNA into chromatin can be repressive to transcription. ATP-dependent chromatin remodelling activities can facilitate transcription from chromatin templates. Consistent with this, biochemical assays have shown that the action of ATP-dependent chromatin remodelling activities increase the accessibility of DNA within chromatin templates. However more recent functional studies suggest that many ATP-dependent chromatin remodelling activities can also function as repressors of transcription. Here we review recent advances to our understanding of the biological function of these complexes. We then consider some of the mechanisms by which ATP-dependent chromatin remodelling activities together with other forms of chromatin remodelling or modifying enzymes may act to regulate genomic accessibility either positively or negatively.

Adenosine Triphosphatases↗

PubMed2000

ATP-dependent chromatin remodeling: going mobile.

Members of the ATP-dependent class of chromatin remodeling enzymes are found in all eukaryotes where they play key roles in many DNA-mediated processes. Each of these enzymes are multi-subunit assembles that hydrolyze approximately 1000 ATP/min. The energy of ATP hydrolysis is used to disrupt the chromatin structure which can be scored by enhanced factor binding, disruption of the DNase I cleavage pattern of mononucleosomes, formation of dinucleosomes, movements of histone octamers in cis and in trans, and by generation of nuclease hypersensitive sites. Here the biochemical properties of these enzymes are reviewed and the manner in which ATP-driven nucleosome movements might account for many of these diverse activities is discussed.

Adenosine Triphosphatases↗

PubMed2006

The protein arginine methyltransferase Prmt5 is required for myogenesis because it facilitates ATP-dependent chromatin remodeling.

Skeletal muscle differentiation requires the coordinated activity of transcription factors, histone modifying enzymes, and ATP-dependent chromatin remodeling enzymes. The type II protein arginine methyltransferase Prmt5 symmetrically dimethylates histones H3 and H4 and numerous nonchromatin proteins, and prior work has implicated Prmt5 in transcriptional repression. Here we demonstrate that MyoD-induced muscle differentiation requires Prmt5. One of the first genes activated during differentiation encodes the myogenic regulator myogenin. Prmt5 and dimethylated H3R8 (histone 3 arginine 8) are localized at the myogenin promoter in differentiating cells. Modification of H3R8 required Prmt5, and reduction of Prmt5 resulted in the abrogation of promoter binding by the Brg1 ATPase-associated with the SWI/SNF chromatin remodeling enzymes and all subsequent events associated with gene activation, including increases in chromatin accessibility and stable binding by MyoD. Prmt5 and dimethylated H3R8 were also associated with the myogenin promoter in activated satellite cells isolated from muscle tissue, further demonstrating the physiological relevance of these observations. The data indicate that Prmt5 facilitates myogenesis because it is required for Brg1-dependent chromatin remodeling and gene activation at a locus essential for differentiation. We therefore conclude that a histone modifying enzyme is necessary to permit an ATP-dependent chromatin remodeling enzyme to function.

Adenosine Triphosphate↗

PubMed2000

Mechanisms for ATP-dependent chromatin remodelling.

Gene regulation involves the generation of a local chromatin topology that is conducive to transcription. Several classes of chromatin remodelling activity have been shown to play a role in this process. ATP-dependent chromatin-remodelling activities use energy derived from the hydrolysis of ATP to alter the structure of chromatin, making it more accessible for transcription factor binding. The yeast SWI-SWF complex is the founding member of this family of ATP-dependent chromatin-remodelling activities. We have developed a model system to study the ability of the SWI-SWF complex to alter chromatin structure. Using this system, we find that SWI-SWF is able to alter the position of nucleosomes along the DNA. This is consistent with recent reports that other ATP-dependent chromatin-remodelling activities can alter the positions of nucleosomes along DNA. This suggests that nucleosome mobilization may be a general feature of the activity of ATP-dependent chromatin-remodelling activities. Some of the mechanisms by which nucleosomes may be moved along DNA are discussed.

Adenosine Triphosphate↗

PubMed2001

Mechanisms for ATP-dependent chromatin remodelling.

During the past year, major advances have been made towards understanding the function of ATP-dependent chromatin-remodelling activities both in vitro and in vivo. These suggest that ATP-dependent chromatin-remodelling activities are capable of both altering the structure of individual nucleosomes and acting in concert with other forms of chromatin-modifying enzymes, to regulate the formation and decondensation of chromatin fibres.

Adenosine Triphosphate↗

PubMed2005

ATP-dependent chromatin remodeling and DNA double-strand break repair.

The repair of DNA double-strand breaks (DSBs) is critical for the maintenance of genomic stability. Two pathways for the repair of DBSs, nonhomologous end-joining (NHEJ) and homologous recombination (HR), have evolved in eukaryotes. These pathways, like processes such as transcription and replication, act on DNA that is embedded in nucleosomes. Recent studies have shown that DNA repair, like transcription, is facilitated both by histone tail modification and by ATP-dependent chromatin remodeling. This review emphasizes recent reports that demonstrate a function for the ATP-dependent chromatin remodeling complexes INO80 and RSC in NHEJ and HR. We also discuss the possible role of SWR1- and TIP60-mediated nucleosomal histone exchange in DNA repair.

Adenosine Triphosphate↗

PubMed2003

Involvement of actin-related proteins in ATP-dependent chromatin remodeling.

Actin-related proteins (Arps) and conventional actin are enigmatic components of many chromatin-remodeling enzyme complexes. The yeast INO80 ATP-dependent chromatin-remodeling complex contains stoichiometric amounts of Arp4, Arp5, Arp8, and actin. Here we have revealed functions of Arp5 and Arp8 by analysis of mutants. arp5 Delta and arp8 Delta mutants display an ino80 Delta phenotype. Purification of INO80 complexes from arp5 Delta and arp8 Delta cells shows that protein complexes remain intact but are compromised for INO80 ATPase activity, DNA binding, and nucleosome mobilization. The INO80 (arp8 Delta) complex is strikingly deficient, not only for the Arp8 subunit, but also for Arp4 and actin, suggesting an ordered assembly of Arps. Binding of Arp8 to the INO80 complex requires an N-terminal region of Ino80 adjacent to the conserved ATPase domain. GST-Arp8 binds preferentially to histones H3 and H4 in vitro, suggesting a histone chaperone function. These findings show direct involvement of Arps in the chromatin-remodeling process.

Actins↗

PubMed2001

The bromodomain: a regulator of ATP-dependent chromatin remodeling?

In eukaryotes, processes requiring access to DNA are inhibited by the structural packaging of the genome. A number of specialized ATP-dependent chromatin remodeling enzymes have evolved to overcome this inhibition. One subset of these enzymes, SWI/SNF, plays a critical role in the regulation of transcription, often functioning in concert with nuclear histone acetyltransferases (HATs). It remains unknown how these activities are coordinated. However, recent results revealing that the bromodomain, a motif common in these remodeling factors, constitutes an acetyl-lysine binding domain might provide insight into this process. Bromodomains may serve a role analogous to the signal transduction SH2 domain, by providing a means to recruit remodeling complexes to acetylated chromatin regions or to allosterically modify their function post-recruitment.

Acetyltransferases↗

PubMed2005

ATP-dependent chromatin remodeling complexes and their role in nuclear receptor-dependent transcription in vivo.

Nuclear receptors (NRs) are ligand-dependent transcription factors that mediate transcription of target genes in chromatin. Modulation of chromatin structure plays an important part in the NR-mediated transcription process. ATP-dependent chromatin remodeling complexes have been shown to be intimately involved in NR-mediated transcription. In this review, we examine the role of chromatin remodeling complexes in facilitating the recruitment of coregulators and basal transcription factors. In addition, the role of subunit specificity within the chromatin remodeling complexes, the complexes' influence on remodeling activity, and complexes' recruitment to the NR-responsive promoters are discussed.

Adenosine Triphosphate↗

PubMed2006

ATP-dependent chromatin remodeling complexes in Drosophila.

The regulation of chromatin structure is of fundamental importance for many DNA-based processes in eukaryotes. Activation or repression of gene transcription or DNA replication depends on enzymes which can generate the appropriate chromatin environment. Several of these enzymes utilize the energy of ATP hydrolysis to alter nucleosome structure. In recent years our understanding of the multisubunit complexes within which they function, their mechanisms of action, their regulation and their in-vivo roles has increased. Much of what we have learned has been gleaned from studies in Drosophila melanogaster. Here we will review what we know about the main classes of ATP-dependent chromatin remodelers in Drosophila.

Adenosine Triphosphatases↗

PubMed2001

ATP-dependent chromatin remodeling facilitates nucleotide excision repair of UV-induced DNA lesions in synthetic dinucleosomes.

To investigate the relationship between chromatin dynamics and nucleotide excision repair (NER), we have examined the effect of chromatin structure on the formation of two major classes of UV-induced DNA lesions in reconstituted dinucleosomes. Furthermore, we have developed a model chromatin-NER system consisting of purified human NER factors and dinucleosome substrates that contain pyrimidine (6-4) pyrimidone photoproducts (6-4PPs) either at the center of the nucleosome or in the linker DNA. We have found that the two classes of UV-induced DNA lesions are formed efficiently at every location on dinucleosomes in a manner similar to that of naked DNA, even in the presence of histone H1. On the other hand, excision of 6-4PPs is strongly inhibited by dinucleosome assembly, even within the linker DNA region. These results provide direct evidence that the human NER machinery requires a space greater than the size of the linker DNA to excise UV lesions efficiently. Interestingly, NER dual incision in dinucleosomes is facilitated by recombinant ACF, an ATP-dependent chromatin remodeling factor. Our results indicate that there is a functional connection between chromatin remodeling and the initiation step of NER.

Adenosine Triphosphatases↗