scholarly journals The DPF Domain As a Unique Structural Unit Participating in Transcriptional Activation, Cell Differentiation, and Malignant Transformation

Acta Naturae ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 57-65
Author(s):  
N. V. Soshnikova ◽  
A. A. Sheynov ◽  
Eu. V. Tatarskiy ◽  
S. G. Georgieva
Keyword(s):  
Malignant Transformation ◽  
Chromatin Remodeling ◽  
Transcriptional Activation ◽  
Mammalian Cells ◽  
Protein Complexes ◽  
Active Chromatin ◽  
Phd Finger ◽  
Chromatin Remodeling Complex ◽  
Single Structure ◽  
Chromatin Proteins

The DPF (double PHD finger) domain consists of two PHD fingers organized in tandem. The two PHD-finger domains within a DPF form a single structure that interacts with the modification of the N-terminal histone fragment in a way different from that for single PHD fingers. Several histone modifications interacting with the DPF domain have already been identified. They include acetylation of H3K14 and H3K9, as well as crotonylation of H3K14. These modifications are found predominantly in transcriptionally active chromatin. Proteins containing DPF belong to two classes of protein complexes, which are the transcriptional coactivators involved in the regulation of the chromatin structure. These are the histone acetyltransferase complex belonging to the MYST family and the SWI/SNF chromatin-remodeling complex. The DPF domain is responsible for the specificity of the interactions between these complexes and chromatin. Proteins containing DPF play a crucial role in the activation of the transcription of a number of genes expressed during the development of an organism. These genes are important in the differentiation and malignant transformation of mammalian cells.

scholarly journals SIRT6 promotes transcription of a subset of NRF2 targets by mono-ADP-ribosylating BAF170

2019 ◽  
Vol 47 (15) ◽  
pp. 7914-7928 ◽  
Author(s):  
Sarallah Rezazadeh ◽  
David Yang ◽  
Gregory Tombline ◽  
Matthew Simon ◽  
Sean P Regan ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Rna Polymerase Ii ◽  
Chromatin Remodeling ◽  
Transcriptional Activation ◽  
Heme Oxygenase 1 ◽  
Nuclear Factor ◽  
Active Chromatin ◽  
Adp Ribosylation ◽  
Chromatin Remodeling Complex ◽  
A Subunit

Abstract SIRT6 is critical for activating transcription of Nuclear factor (erythroid-derived 2)-like 2 (NRF2) responsive genes during oxidative stress. However, while the mechanism of SIRT6-mediated silencing is well understood, the mechanism of SIRT6-mediated transcriptional activation is unknown. Here, we employed SIRT6 separation of function mutants to reveal that SIRT6 mono-ADP-ribosylation activity is required for transcriptional activation. We demonstrate that SIRT6 mono-ADP-ribosylation of BAF170, a subunit of BAF chromatin remodeling complex, is critical for activation of a subset of NRF2 responsive genes upon oxidative stress. We show that SIRT6 recruits BAF170 to enhancer region of the Heme oxygenase-1 locus and promotes recruitment of RNA polymerase II. Furthermore, SIRT6 mediates the formation of the active chromatin 10-kb loop at the HO-1 locus, which is absent in SIRT6 deficient tissue. These results provide a novel mechanism for SIRT6-mediated transcriptional activation, where SIRT6 mono-ADP-ribosylates and recruits chromatin remodeling proteins to mediate the formation of active chromatin loop.

scholarly journals The Swi/Snf Chromatin Remodeling Complex Is Required for Ribosomal DNA and Telomeric Silencing in Saccharomyces cerevisiae

2004 ◽  
Vol 24 (18) ◽  
pp. 8227-8235 ◽  
Author(s):  
Vardit Dror ◽  
Fred Winston
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Chromatin Remodeling ◽  
Ribosomal Dna ◽  
Transcriptional Activation ◽  
Rdna Locus ◽  
Detectable Effect ◽  
Chromatin Remodeling Complex ◽  
Two Factors

ABSTRACT The Swi/Snf chromatin remodeling complex has been previously demonstrated to be required for transcriptional activation and repression of a subset of genes in Saccharomyces cerevisiae. In this work we demonstrate that Swi/Snf is also required for repression of RNA polymerase II-dependent transcription in the ribosomal DNA (rDNA) locus (rDNA silencing). This repression appears to be independent of both Sir2 and Set1, two factors known to be required for rDNA silencing. In contrast to many other rDNA silencing mutants that have elevated levels of rDNA recombination, snf2Δ mutants have a significantly decreased level of rDNA recombination. Additional studies have demonstrated that Swi/Snf is also required for silencing of genes near telomeres while having no detectable effect on silencing of HML or HMR.

scholarly journals Efg1-mediated Recruitment of NuA4 to Promoters Is Required for Hypha-specific Swi/Snf Binding and Activation inCandida albicans

2008 ◽  
Vol 19 (10) ◽  
pp. 4260-4272 ◽  
Author(s):  
Yang Lu ◽  
Chang Su ◽  
Xuming Mao ◽  
Prashna Pala Raniga ◽  
Haoping Liu ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Transcriptional Activation ◽  
Chromatin Immunoprecipitation ◽  
Pathogenic Fungus ◽  
Dependent Manner ◽  
Hyphal Development ◽  
Chromatin Remodeling Complex ◽  
A Subunit ◽  
Human Pathogenic Fungus ◽  
Incandida Albicans

Efg1 is essential for hyphal development and virulence in the human pathogenic fungus Candida albicans. How Efg1 regulates gene expression is unknown. Here, we show that Efg1 interacts with components of the nucleosome acetyltransferase of H4 (NuA4) histone acetyltransferase (HAT) complex in both yeast and hyphal cells. Deleting YNG2, a subunit of the NuA4 HAT module, results in a significant decrease in the acetylation level of nucleosomal H4 and a profound defect in hyphal development, as well as a defect in the expression of hypha-specific genes. Using chromatin immunoprecipitation, Efg1 and the NuA4 complex are found at the UAS regions of hypha-specific genes in both yeast and hyphal cells, and Efg1 is required for the recruitment of NuA4. Nucleosomal H4 acetylation at the promoters peaks during initial hyphal induction in an Efg1-dependent manner. We also find that Efg1 bound to the promoters of hypha-specific genes is critical for recruitment of the Swi/Snf chromatin remodeling complex during hyphal induction. Our data show that the recruitment of the NuA4 complex by Efg1 to the promoters of hypha-specific genes is required for nucleosomal H4 acetylation at the promoters during hyphal induction and for subsequent binding of Swi/Snf and transcriptional activation.

Nuclear receptor coactivators: the key to unlock chromatin

2005 ◽  
Vol 83 (4) ◽  
pp. 418-428 ◽  
Author(s):  
Wei Xu
Keyword(s):  
Nuclear Receptors ◽  
Nuclear Receptor ◽  
Chromatin Remodeling ◽  
Transcriptional Activation ◽  
Transcriptional Control ◽  
Biological Effects ◽  
Gene Activation ◽  
Nuclear Hormone Receptor ◽  
Nuclear Receptor Coactivators ◽  
Chromatin Remodeling Complex

The biological effects of hormones, ranging from organogenesis, metabolism, and proliferation, are transduced through nuclear receptors (NRs). Over the last decade, NRs have been used as a model to study transcriptional control. The conformation of activated NRs is favorable for the recruitment of coactivators, which promote transcriptional activation by directly communicating with chromatin. This review will focus on the function of different classes of coactivators and associated complexes, and on progress in our understanding of gene activation by NRs through chromatin remodeling.Key words: nuclear hormone receptor, p160 family of coactivators, histone modification, chromatin remodeling complex.

scholarly journals Interaction of Papillomavirus E2 Protein with the Brm Chromatin Remodeling Complex Leads to Enhanced Transcriptional Activation

2006 ◽  
Vol 81 (5) ◽  
pp. 2213-2220 ◽  
Author(s):  
R. Ajay Kumar ◽  
Samisubbu R. Naidu ◽  
Xiaoyu Wang ◽  
Anthony N. Imbalzano ◽  
Elliot J. Androphy
Keyword(s):  
Chromatin Remodeling ◽  
Transcriptional Activation ◽  
Potential Interaction ◽  
Transactivation Domain ◽  
Reporter System ◽  
Barr Virus ◽  
Amino Terminal ◽  
Chromatin Remodeling Complex ◽  
Epstein Barr

ABSTRACT Papillomavirus E2 is a sequence-specific DNA binding protein that regulates transcription and replication of the viral genome. The transcriptional activities of E2 are typically evaluated by transient transfection of nonreplicating E2-dependent reporters. We sought to address whether E2 activates transcription in an episomal context and its potential interaction with the chromatin remodeling proteins. Using an Epstein-Barr virus-based episomal reporter, we demonstrate that E2 stimulates transcription from an E2-dependent promoter in a chromatin context. This activation is enhanced by the presence of proteins associated with SWI/SNF complexes, which are ATP-dependent chromatin remodeling enzymes. We show that exogenous expression of the Brm ATPase enhances E2 activity in SWI/SNF-deficient cell lines and that the amino-terminal transactivation domain of E2 mediates association with the Brm complex in vivo. Using chromatin immunoprecipitation assays, we demonstrate that Brm enhances promoter occupancy by E2 in an episomal context. Our results demonstrate that E2 activates transcription from an episomal reporter system and reveal a novel property of E2 in collaborating with the Brm chromatin remodeling complex in enhancing transcriptional activation.

scholarly journals Conserved Structure and Evolution of DPF Domain of PHF10—The Specific Subunit of PBAF Chromatin Remodeling Complex

2021 ◽  
Vol 22 (20) ◽  
pp. 11134
Author(s):  
Anton O. Chugunov ◽  
Nadezhda A. Potapova ◽  
Natalia S. Klimenko ◽  
Victor V. Tatarskiy ◽  
Sofia G. Georgieva ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Histone Modifications ◽  
Transcription Activation ◽  
Sequence Structure ◽  
Histone Tails ◽  
Phd Finger ◽  
Chromatin Remodeling Complex ◽  
Regulation Functions ◽  
Distinct Features ◽  
Structure And Functions

Transcription activation factors and multisubunit coactivator complexes get recruited at specific chromatin sites via protein domains that recognize histone modifications. Single PHDs (plant homeodomains) interact with differentially modified H3 histone tails. Double PHD finger (DPF) domains possess a unique structure different from PHD and are found in six proteins: histone acetyltransferases MOZ and MORF; chromatin remodeling complex BAF (DPF1–3); and chromatin remodeling complex PBAF (PHF10). Among them, PHF10 stands out due to the DPF sequence, structure, and functions. PHF10 is ubiquitously expressed in developing and adult organisms as four isoforms differing in structure (the presence or absence of DPF) and transcription regulation functions. Despite the importance of the DPF domain of PHF10 for transcription activation, its structure remains undetermined. We performed homology modeling of the human PHF10 DPF domain and determined common and distinct features in structure and histone modifications recognition capabilities, which can affect PBAF complex chromatin recruitment. We also traced the evolution of DPF1–3 and PHF10 genes from unicellular to vertebrate organisms. The data reviewed suggest that the DPF domain of PHF10 plays an important role in SWI/SNF-dependent chromatin remodeling during transcription activation.

scholarly journals Cryo-electron microscopy structure of a nucleosome-bound SWI/SNF chromatin remodeling complex

2019 ◽  
Author(s):  
Yan Han ◽  
Alexis A Reyes ◽  
Sara Malik ◽  
Yuan He
Keyword(s):  
Electron Microscopy ◽  
Chromatin Remodeling ◽  
Atp Hydrolysis ◽  
Protein Complexes ◽  
Gene Activation ◽  
The Body ◽  
Cellular Processes ◽  
Cryo Electron Microscopy ◽  
Chromatin Remodeling Complex ◽  
High Resolution Structure

AbstractThe multi-subunit chromatin remodeling complex SWI/SNF1–3 is highly conserved from yeast to humans and plays critical roles in various cellular processes including transcription and DNA damage repair4, 5. It uses the energy from ATP hydrolysis to remodel chromatin structure by sliding and evicting the histone octamer6–10, creating DNA regions that become accessible to other essential protein complexes. However, our mechanistic understanding of the chromatin remodeling activity is largely hindered by the lack of a high-resolution structure of any complex from this family. Here we report the first structure of SWI/SNF from the yeast S. cerevisiae bound to a nucleosome at near atomic resolution determined by cryo-electron microscopy (cryo-EM). In the structure, the Arp module is sandwiched between the ATPase and the Body module of the complex, with the Snf2 HSA domain connecting all modules. The HSA domain also extends into the Body and anchors at the opposite side of the complex. The Body contains an assembly scaffold composed of conserved subunits Snf12 (SMARCD/BAF60), Snf5 (SMARCB1/BAF47/ INI1) and an asymmetric dimer of Swi3 (SMARCC/BAF155/170). Another conserved subunit Swi1 (ARID1/BAF250) folds into an Armadillo (ARM) repeat domain that resides in the core of the SWI/SNF Body, acting as a molecular hub. In addition to the interaction between Snf2 and the nucleosome, we also observed interactions between the conserved Snf5 subunit and the histones at the acidic patch, which could serve as an anchor point during active DNA translocation. Our structure allows us to map and rationalize a subset of cancer-related mutations in the human SWI/SNF complex and propose a model of how SWI/SNF recognizes and remodels the +1 nucleosome to generate nucleosome-depleted regions during gene activation11–13.

Chromatin Boundaries Require the Functional Cooperation Between hSET1 and NURF Complexes

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 646-646
Author(s):  
Xingguo Li ◽  
Shaohua Wang ◽  
Ying Li ◽  
Yi Qiu ◽  
Suming Huang
Keyword(s):  
Chromatin Remodeling ◽  
Conflicts Of Interest ◽  
Protein Complexes ◽  
Chromatin Modification ◽  
Rapid Loss ◽  
Active Chromatin ◽  
Chromatin Insulator ◽  
Knock Down ◽  
Histone H3k4 ◽  
H3k9 Dimethylation

Abstract Abstract 646 Chromatin modification and remodeling activities play a central role in organizing nuclear functions in eukaryotic genome. Chromatin domains with characteristic epigenetic marks are organized by chromatin insulator. The chicken b-globin insulator, 5′HS4, is an excellent model system to study how insulator maintains gene function and prevents the encroachment of repressive heterochromatin. We showed previously that USF1/2 bound 5′HS4 insulator mediates chromatin barrier activity by recruiting and organizing active histone modifications in the chicken b-globin locus. However, it is not clear how insulator establishes such a barrier. To further understand the physical function of USF1, we purified the USF1-associated protein complexes. We found that USF1 forms a multiprotein complex with hSET1 and NURF exhibiting histone H3K4 methyltransferase and ATP-dependent chromatin remodeling activities, respectively. Both hSET1 and NURF complexes are specifically recruited to the 5′HS4 insulator by USF1 to retain the active chromatin structure. Knock-down of BPTF, a component of NURF complex, resulted in a rapid loss of barrier activity that protects a transgene from chromatin silencing. The loss of barrier by the BPTF knock-down is accompanied by an alternation of nucleosome positioning that expands the nucleosome to the nucleosome free linker region in the HS4 insulator site and increases repressive H3K9 dimethylation. Furthermore, the suppression of hSET1, a H3K4 methyltransferase, leads to not only a loss of barrier activity, but also a loss of H3K4 dimethylation and H3K9/K14 acetylation, as well as the recruitment of BPTF at chromatin insulator sites. Thus, our data reveal a molecular mechanism in which histone modifying enzyme hSET1 and chromatin remodeling complex NURF collaborate together to maintain the 5′HS4 chromatin barrier activity and to prevent the encroachment of adjacent heterochromatin. Disclosures: No relevant conflicts of interest to declare.

Nucleosome organization and targeting of SWI/SNF chromatin-remodeling complexes: contributions of the DNA sequenceThis paper is one of a selection of papers published in this Special Issue, entitled 28th International West Coast Chromatin and Chromosomes Conference, and has undergone the Journal's usual peer review process.

2007 ◽  
Vol 85 (4) ◽  
pp. 419-425 ◽  
Author(s):  
Martin Montecino ◽  
Janet L. Stein ◽  
Gary S. Stein ◽  
Jane B. Lian ◽  
Andre J. van Wijnen ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Transcriptional Activation ◽  
Molecular Mechanisms ◽  
Protein Complexes ◽  
Peer Review Process ◽  
Gene Promoter ◽  
Limited Attention ◽  
Dependent Manner ◽  
Nucleosome Remodeling ◽  
Eukaryotic Genes

Chromatin organization within the nuclear compartment is a fundamental mechanism to regulate the expression of eukaryotic genes. During the last decade, a number of nuclear protein complexes with the ability to remodel chromatin and regulate gene transcription have been reported. Among these complexes is the SWI/SNF family, which alters chromatin structure in an ATP-dependent manner. A considerable effort has been made to understand the molecular mechanisms by which SWI/SNF catalyzes nucleosome remodeling. However, limited attention has been dedicated to studying the role of the DNA sequence in this remodeling process. Therefore, in this minireview, we discuss the contribution of nucleosome positioning and nucleosome excluding sequences to the targeting and activity of SWI/SNF complexes. This discussion includes results from our group using the rat osteocalcin gene promoter as a model. Based on these results, we postulate a model for chromatin remodeling and transcriptional activation of this gene in osteoblastic cells.

scholarly journals Molecular Basis of Histone Tail Recognition by Human TIP5 PHD Finger and Bromodomain of the Chromatin Remodeling Complex NoRC

Structure ◽  
2015 ◽  
Vol 23 (1) ◽  
pp. 80-92 ◽  
Author(s):  
Cynthia Tallant ◽  
Erica Valentini ◽  
Oleg Fedorov ◽  
Lois Overvoorde ◽  
Fleur M. Ferguson ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Molecular Basis ◽  
Histone Tail ◽  
Phd Finger ◽  
Chromatin Remodeling Complex
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