scholarly journals The Molecular Basis of Specific DNA Binding by the BRG1 AT-hook and Bromodomain

2019 ◽  
Author(s):  
Julio C. Sanchez ◽  
Liyang Zhang ◽  
Stefania Evoli ◽  
Nicholas J. Schnicker ◽  
Maria Nunez-Hernandez ◽  
...  
Keyword(s):  
Dna Binding ◽  
Chromatin Remodeling ◽  
Critical Role ◽  
Binding Pocket ◽  
Structural Basis ◽  
Atpase Subunit ◽  
Baf Complex ◽  
Chromatin Remodeling Complex ◽  
Cancer Mutations ◽  
Dna Specificity

AbstractThe ATP-dependent BAF chromatin remodeling complex plays a critical role in gene regulation by modulating chromatin architecture, and is frequently mutated in cancer. Indeed, subunits of the BAF complex are found to be mutated in >20% of human tumors. The mechanism by which BAF properly navigates chromatin is not fully understood, but is thought to involve a multivalent network of histone and DNA contacts. We previously identified a composite domain in the BRG1 ATPase subunit that is capable of associating with both histones and DNA in a multivalent manner. Mapping the DNA binding pocket revealed that it contains several cancer mutations. Here, we utilize SELEX-seq to identify the DNA specificity of this composite domain and NMR spectroscopy and molecular modelling to determine the structural basis of DNA binding. Finally, we demonstrate that cancer mutations in this domain alter the mode of DNA association.

scholarly journals Rely on Each Other: DNA Binding Cooperativity Shapes p53 Functions in Tumor Suppression and Cancer Therapy

Cancers ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 2422
Author(s):  
Oleg Timofeev ◽  
Thorsten Stiewe
Keyword(s):  
Cancer Therapy ◽  
Dna Binding ◽  
Cell Fate ◽  
Tumor Suppression ◽  
Quaternary Structure ◽  
Three Dimensional ◽  
Structural Basis ◽  
Sequence Specificity ◽  
Cell Fate Decisions ◽  
Cancer Mutations

p53 is a tumor suppressor that is mutated in half of all cancers. The high clinical relevance has made p53 a model transcription factor for delineating general mechanisms of transcriptional regulation. p53 forms tetramers that bind DNA in a highly cooperative manner. The DNA binding cooperativity of p53 has been studied by structural and molecular biologists as well as clinical oncologists. These experiments have revealed the structural basis for cooperative DNA binding and its impact on sequence specificity and target gene spectrum. Cooperativity was found to be critical for the control of p53-mediated cell fate decisions and tumor suppression. Importantly, an estimated number of 34,000 cancer patients per year world-wide have mutations of the amino acids mediating cooperativity, and knock-in mouse models have confirmed such mutations to be tumorigenic. While p53 cancer mutations are classically subdivided into “contact” and “structural” mutations, “cooperativity” mutations form a mechanistically distinct third class that affect the quaternary structure but leave DNA contacting residues and the three-dimensional folding of the DNA-binding domain intact. In this review we discuss the concept of DNA binding cooperativity and highlight the unique nature of cooperativity mutations and their clinical implications for cancer therapy.

scholarly journals Crystallization of and selenomethionine phasing strategy for a SETMAR–DNA complex

2016 ◽  
Vol 72 (9) ◽  
pp. 713-719 ◽  
Author(s):  
Qiujia Chen ◽  
Millie Georgiadis
Keyword(s):  
Dna Binding ◽  
Catalytic Domain ◽  
Specific Binding ◽  
Critical Role ◽  
Binding Activity ◽  
Structural Basis ◽  
Unexpected Finding ◽  
Terminal Inverted Repeat ◽  
Dna Binding Activity ◽  
New Genes

Transposable elements have played a critical role in the creation of new genes in all higher eukaryotes, including humans. Although the chimeric fusion protein SETMAR is no longer active as a transposase, it contains both the DNA-binding domain (DBD) and catalytic domain of theHsmar1transposase. The amino-acid sequence of the DBD has been virtually unchanged in 50 million years and, as a consequence, SETMAR retains its sequence-specific binding to the ancestralHsmar1terminal inverted repeat (TIR) sequence. Thus, the DNA-binding activity of SETMAR is likely to have an important biological function. To determine the structural basis for the recognition of TIR DNA by SETMAR, the design of TIR-containing oligonucleotides and SETMAR DBD variants, crystallization of DBD–DNA complexes, phasing strategies and initial phasing experiments are reported here. An unexpected finding was that oligonucleotides containing two BrdUs in place of thymidines produced better quality crystals in complex with SETMAR than their natural counterparts.

scholarly journals Critical role of Brg1 member of the SWI/SNF chromatin remodeling complex during neurogenesis and neural crest induction in zebrafish

2006 ◽  
Vol 235 (10) ◽  
pp. 2722-2735 ◽  
Author(s):  
Binnur Eroglu ◽  
Guanghu Wang ◽  
Naxin Tu ◽  
Xutong Sun ◽  
Nahid F. Mivechi
Keyword(s):  
Neural Crest ◽  
Chromatin Remodeling ◽  
Critical Role ◽  
Chromatin Remodeling Complex

The trithorax group gene osa encodes an ARID-domain protein that genetically interacts with the brahma chromatin-remodeling factor to regulate transcription

Development ◽  
1999 ◽  
Vol 126 (4) ◽  
pp. 733-742 ◽  
Author(s):  
M. Vazquez ◽  
L. Moore ◽  
J.A. Kennison
Keyword(s):  
Gene Regulation ◽  
Chromatin Remodeling ◽  
Homeotic Gene ◽  
Dna Binding Domain ◽  
Atpase Subunit ◽  
Trithorax Group ◽  
Chromatin Remodeling Complex ◽  
P2 Promoter ◽  
Domain Protein ◽  
Arid Domain

The trithorax group gene brahma (brm) encodes the ATPase subunit of a chromatin-remodeling complex involved in homeotic gene regulation. We report here that brm interacts with another trithorax group gene, osa, to regulate the expression of the Antennapedia P2 promoter. Regulation of Antennapedia by BRM and OSA proteins requires sequences 5′ to the P2 promoter. Loss of maternal osa function causes severe segmentation defects, indicating that the function of osa is not limited to homeotic gene regulation. The OSA protein contains an ARID domain, a DNA-binding domain also present in the yeast SWI1 and Drosophila DRI proteins. We propose that the OSA protein may target the BRM complex to Antennapedia and other regulated genes.

Brg1, the ATPase subunit of the SWI/SNF chromatin remodeling complex, is required for myeloid differentiation to granulocytes

2005 ◽  
Vol 206 (1) ◽  
pp. 112-118 ◽  
Author(s):  
Diana Vradii ◽  
Stefan Wagner ◽  
Diem N. Doan ◽  
Jeffrey A. Nickerson ◽  
Martin Montecino ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Myeloid Differentiation ◽  
Atpase Subunit ◽  
Chromatin Remodeling Complex

scholarly journals The Structural Basis for Glycerol Permeation by human AQP7

2019 ◽  
Author(s):  
Li Zhang ◽  
Deqiang Yao ◽  
Fu Zhou ◽  
Qing Zhang ◽  
Ying Xia ◽  
...  
Keyword(s):  
Physiological Condition ◽  
Critical Role ◽  
Binding Pocket ◽  
Structural Basis ◽  
Glycerol Metabolism ◽  
Functional Assay ◽  
Substrate Binding Pocket ◽  
Glycerol Molecule ◽  
Cytoplasmic Side

AbstractHuman glycerol channel AQP7 conducts glycerol release from adipocyte and entry into the cells in pancreatic islets, muscles and kidney tubule, and thus regulate glycerol metabolism in those tissues. Compared with other human aquaglyceroporins, AQP7 shows a less conserved “NPA” motif in the center cavity, and a pair of aromatic residues at Ar/R selectivity filter. To understand the structural basis for the glycerol conductance, we crystallized the human AQP7 and determined the structure at 3.7 Å. A substrate binding pocket was found near to the Ar/R filter and the bound glycerol molecule stabilized by R229. In vivo functional assay on human AQP7 as well as AQP3 and AQP10 demonstrated strong glycerol transportation activities at physiological condition. The human AQP7 structure reveals a fully closed conformation with its permeation pathway strictly confined by Ar/R filter at the exoplasmic side and the gate at the cytoplasmic side, and the dislocation of the residues at narrowest parts of glycerol pathway in AQP7 play a critical role in controlling the glycerol flux.

scholarly journals An Ikaros-Containing Chromatin-Remodeling Complex in Adult-Type Erythroid Cells

2000 ◽  
Vol 20 (20) ◽  
pp. 7572-7582 ◽  
Author(s):  
David W. O'Neill ◽  
Stuti S. Schoetz ◽  
Rocio A. Lopez ◽  
Madalyn Castle ◽  
Lisa Rabinowitz ◽  
...  
Keyword(s):  
Dna Binding ◽  
Chromatin Remodeling ◽  
Dna Sequences ◽  
Globin Gene ◽  
Binding Activity ◽  
Erythroid Cells ◽  
Adult Type ◽  
Nucleosome Remodeling ◽  
Dna Binding Activity ◽  
Chromatin Remodeling Complex

ABSTRACT We have previously described a SWI/SNF-related protein complex (PYR complex) that is restricted to definitive (adult-type) hematopoietic cells and that specifically binds DNA sequences containing long stretches of pyrimidines. Deletion of an intergenic DNA-binding site for this complex from a human β-globin locus construct results in delayed human γ- to β-globin switching in transgenic mice, suggesting that the PYR complex acts to facilitate the switch. We now show that PYR complex DNA-binding activity also copurifies with subunits of a second type of chromatin-remodeling complex, nucleosome-remodeling deacetylase (NuRD), that has been shown to have both nucleosome-remodeling and histone deacetylase activities. Gel supershift assays using antibodies to the ATPase-helicase subunit of the NuRD complex, Mi-2 (CHD4), confirm that Mi-2 is a component of the PYR complex. In addition, we show that the hematopoietic cell-restricted zinc finger protein Ikaros copurifies with PYR complex DNA-binding activity and that antibodies to Ikaros also supershift the complex. We also show that NuRD and SWI/SNF components coimmunopurify with each other as well as with Ikaros. Competition gel shift experiments using partially purified PYR complex and recombinant Ikaros protein indicate that Ikaros functions as a DNA-binding subunit of the PYR complex. Our results suggest that Ikaros targets two types of chromatin-remodeling factors—activators (SWI/SNF) and repressors (NuRD)—in a single complex (PYR complex) to the β-globin locus in adult erythroid cells. At the time of the switch from fetal to adult globin production, the PYR complex is assembled and may function to repress γ-globin gene expression and facilitate γ- to β-globin switching.

scholarly journals Eda-activated RelB recruits an SWI/SNF (BAF) chromatin-remodeling complex and initiates gene transcription in skin appendage formation

2018 ◽  
Vol 115 (32) ◽  
pp. 8173-8178 ◽  
Author(s):  
Jian Sima ◽  
Zhijiang Yan ◽  
Yaohui Chen ◽  
Elin Lehrmann ◽  
Yongqing Zhang ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Gene Transcription ◽  
Target Genes ◽  
Specific Gene ◽  
Open Chromatin ◽  
Transcription Profiling ◽  
Baf Complex ◽  
Skin Appendage ◽  
Chromatin Remodeling Complex ◽  
Appendage Formation

Ectodysplasin A (Eda) signaling activates NF-κB during skin appendage formation, but how Eda controls specific gene transcription remains unclear. Here, we find that Eda triggers the formation of an NF-κB–associated SWI/SNF (BAF) complex in which p50/RelB recruits a linker protein, Tfg, that interacts with BAF45d in the BAF complex. We further reveal that Tfg is initially induced by Eda-mediated RelB activation and then bridges RelB and BAF for subsequent gene regulation. The BAF component BAF250a is particularly up-regulated in skin appendages, and epidermal knockout of BAF250a impairs skin appendage development, resulting in phenotypes similar to those of Eda-deficient mouse models. Transcription profiling identifies several target genes regulated by Eda, RelB, and BAF. Notably, RelB and the BAF complex are indispensable for transcription of Eda target genes, and both BAF complex and Eda signaling are required to open chromatin of Eda targets. Our studies thus suggest that Eda initiates a signaling cascade and recruits a BAF complex to specific gene loci to facilitate transcription during organogenesis.

scholarly journals A novel genetic strategy reveals unexpected roles of the Swi–Snf–like chromatin-remodeling BAF complex in thymocyte development

2008 ◽  
Vol 205 (12) ◽  
pp. 2813-2825 ◽  
Author(s):  
Anant Jani ◽  
Mimi Wan ◽  
Jianmin Zhang ◽  
Kairong Cui ◽  
Jie Wu ◽  
...  
Keyword(s):  
Point Mutation ◽  
Chromatin Remodeling ◽  
Target Gene ◽  
General Strategy ◽  
Thymocyte Development ◽  
Atpase Subunit ◽  
Baf Complex ◽  
Chromatin Template ◽  
Mammalian Genetics ◽  
Physical Interactions

We have developed a general strategy for creating littermates bearing either a tissue-specific point mutation or deletion in any target gene, and used the method to dissect the roles of Brg, the ATPase subunit of the chromatin-remodeling Brg-associated factor (BAF) complex, in early thymocyte development. We found that a point mutation that inactivates the Brg ATPase recapitulates multiple defects previously described for Brg deletion (Chi, T.H., M. Wan, P.P. Lee, K. Akashi, D. Metzger, P. Chambon, C.B. Wilson, and G.R. Crabtree. 2003. Immunity. 19:169–182). However, the point mutant helps reveal unexpected roles of Brg in CD25 repression and CD4 activation. Surprisingly, CD4 activation occurs independently of the Brg ATPase and is perhaps mediated by physical interactions between Brg and the CD4 locus. Our study thus suggests that the BAF complex harbors novel activities that can be necessary and even sufficient for stimulating transcription from an endogenous chromatin template in the absence of Brg-dependent remodeling of that template. We conclude that conditional point mutants, rarely used in mammalian genetics, can help uncover important gene functions undetectable or overlooked in deletion mutants.

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