scholarly journals Architecture of the SWI/SNF-Nucleosome Complex

2008 ◽  
Vol 28 (19) ◽  
pp. 6010-6021 ◽  
Author(s):  
Mekonnen Lemma Dechassa ◽  
Bei Zhang ◽  
Rachel Horowitz-Scherer ◽  
Jim Persinger ◽  
Christopher L. Woodcock ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Catalytic Subunit ◽  
Cross Linking ◽  
Dependent Manner ◽  
Transcription Activator ◽  
Entry Site ◽  
Dna Footprinting ◽  
Histone Octamer ◽  
Nucleosomal Dna ◽  
Protein Cross Linking

ABSTRACT The SWI/SNF complex disrupts and mobilizes chromatin in an ATP-dependent manner. SWI/SNF interactions with nucleosomes were mapped by DNA footprinting and site-directed DNA and protein cross-linking when SWI/SNF was recruited by a transcription activator. SWI/SNF was found by DNA footprinting to contact tightly around one gyre of DNA spanning ∼50 bp from the nucleosomal entry site to near the dyad axis. The DNA footprint is consistent with nucleosomes binding to an asymmetric trough of SWI/SNF that was revealed by the improved imaging of free SWI/SNF. The DNA site-directed cross-linking revealed that the catalytic subunit Swi2/Snf2 is associated with nucleosomes two helical turns from the dyad axis and that the Snf6 subunit is proximal to the transcription factor recruiting SWI/SNF. The highly conserved Snf5 subunit associates with the histone octamer and not with nucleosomal DNA. The model of the binding trough of SWI/SNF illustrates how nucleosomal DNA can be mobilized while SWI/SNF remains bound.

scholarly journals Persistent Interactions of Core Histone Tails with Nucleosomal DNA following Acetylation and Transcription Factor Binding

1998 ◽  
Vol 18 (11) ◽  
pp. 6293-6304 ◽  
Author(s):  
Vesco Mutskov ◽  
Delphine Gerber ◽  
Dimitri Angelov ◽  
Juan Ausio ◽  
Jerry Workman ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Molecular Biology ◽  
Binding Sites ◽  
Cross Linking ◽  
Uv Laser ◽  
Histone Tail ◽  
Histone Tails ◽  
Nucleosomal Dna ◽  
Core Histones

ABSTRACT In this study, we examined the effect of acetylation of the NH2 tails of core histones on their binding to nucleosomal DNA in the absence or presence of bound transcription factors. To do this, we used a novel UV laser-induced protein-DNA cross-linking technique, combined with immunochemical and molecular biology approaches. Nucleosomes containing one or five GAL4 binding sites were reconstituted with hypoacetylated or hyperacetylated core histones. Within these reconstituted particles, UV laser-induced histone-DNA cross-linking was found to occur only via the nonstructured histone tails and thus presented a unique tool for studying histone tail interactions with nucleosomal DNA. Importantly, these studies demonstrated that the NH2 tails were not released from nucleosomal DNA upon histone acetylation, although some weakening of their interactions was observed at elevated ionic strengths. Moreover, the binding of up to five GAL4-AH dimers to nucleosomes occupying the central 90 bp occurred without displacement of the histone NH2 tails from DNA. GAL4-AH binding perturbed the interaction of each histone tail with nucleosomal DNA to different degrees. However, in all cases, greater than 50% of the interactions between the histone tails and DNA was retained upon GAL4-AH binding, even if the tails were highly acetylated. These data illustrate an interaction of acetylated or nonacetylated histone tails with DNA that persists in the presence of simultaneously bound transcription factors.

scholarly journals Nucleosome Remodeling by the Human SWI/SNF Complex Requires Transient Global Disruption of Histone-DNA Interactions

2002 ◽  
Vol 22 (11) ◽  
pp. 3653-3662 ◽  
Author(s):  
Sayura Aoyagi ◽  
Geeta Narlikar ◽  
Chunyang Zheng ◽  
Saïd Sif ◽  
Robert E. Kingston ◽  
...  
Keyword(s):  
Restriction Enzyme ◽  
Atp Hydrolysis ◽  
Dnase I ◽  
Cross Linking ◽  
Dna Interactions ◽  
Nucleosome Remodeling ◽  
Histone Octamer ◽  
Nucleosomal Dna ◽  
Single Cross ◽  
A Site

ABSTRACT We utilized a site-specific cross-linking technique to investigate the mechanism of nucleosome remodeling by hSWI/SNF. We found that a single cross-link between H2B and DNA virtually eliminates the accumulation of stably remodeled species as measured by restriction enzyme accessibility assays. However, cross-linking the histone octamer to nucleosomal DNA does not inhibit remodeling as monitored by DNase I digestion assays. Importantly, we found that the restriction enzyme-accessible species can be efficiently cross-linked after remodeling and that the accessible state does not require continued ATP hydrolysis. These results imply that the generation of stable remodeled states requires at least transient disruption of histone-DNA interactions throughout the nucleosome, while hSWI/SNF-catalyzed disruption of just local histone-DNA interactions yields less-stable remodeled states that still display an altered DNase I cleavage pattern. The implications of these results for models of the mechanism of SWI/SNF-catalyzed nucleosome remodeling are discussed.

scholarly journals Plastidial metabolite MEcPP induces a transcriptionally centered stress-response hub via the transcription factor CAMTA3

2016 ◽  
Vol 113 (31) ◽  
pp. 8855-8860 ◽  
Author(s):  
Geoffrey Benn ◽  
Marta Bjornson ◽  
Haiyan Ke ◽  
Amancio De Souza ◽  
Edward I. Balmond ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Stress Response ◽  
Large Scale ◽  
Leucine Zipper ◽  
Dependent Manner ◽  
Adaptive Responses ◽  
Transcription Activator ◽  
Basic Leucine Zipper ◽  
Environmental Signals ◽  
Calmodulin Binding

The general stress response (GSR) is an evolutionarily conserved rapid and transient transcriptional reprograming of genes central for transducing environmental signals into cellular responses, leading to metabolic and physiological readjustments to cope with prevailing conditions. Defining the regulatory components of the GSR will provide crucial insight into the design principles of early stress-response modules and their role in orchestrating master regulators of adaptive responses. Overaccumulation of methylerythritol cyclodiphosphate (MEcPP), a bifunctional chemical entity serving as both a precursor of isoprenoids produced by the plastidial methylerythritol phosphate (MEP) pathway and a stress-specific retrograde signal, in ceh1 (constitutively expressing hydroperoxide lyase1)-mutant plants leads to large-scale transcriptional alterations. Bioinformatic analyses of microarray data in ceh1 plants established the overrepresentation of a stress-responsive cis element and key GSR marker, the rapid stress response element (RSRE), in the promoters of robustly induced genes. ceh1 plants carrying an established 4×RSRE:Luciferase reporter for monitoring the GSR support constitutive activation of the response in this mutant background. Genetics and pharmacological approaches confirmed the specificity of MEcPP in RSRE induction via the transcription factor CALMODULIN-BINDING TRANSCRIPTION ACTIVATOR 3 (CAMTA3), in a calcium-dependent manner. Moreover, CAMTA3-dependent activation of IRE1a (inositol-requiring protein-1) and bZIP60 (basic leucine zipper 60), two RSRE containing unfolded protein-response genes, bridges MEcPP-mediated GSR induction to the potentiation of protein-folding homeostasis in the endoplasmic reticulum. These findings introduce the notion of transcriptional regulation by a key plastidial retrograde signaling metabolite that induces nuclear GSR, thereby offering a window into the role of interorgannellar communication in shaping cellular adaptive responses.

Transglutaminase-Catalyzed Protein-Protein Cross-Linking Suppresses the Activity of the NF- B-Like Transcription Factor Relish

2013 ◽  
Vol 6 (285) ◽  
pp. ra61-ra61 ◽  
Author(s):  
T. Shibata ◽  
S. Sekihara ◽  
T. Fujikawa ◽  
R. Miyaji ◽  
K. Maki ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Cross Linking ◽  
Protein Cross Linking

scholarly journals Targets of the Gal4 Transcription Activator in Functional Transcription Complexes

2005 ◽  
Vol 25 (20) ◽  
pp. 9092-9102 ◽  
Author(s):  
Wendy M. Reeves ◽  
Steven Hahn
Keyword(s):  
Gene Regulation ◽  
Transcription Factor ◽  
Transcription Activation ◽  
Cross Linking ◽  
Transcription Activator ◽  
Physical Proximity ◽  
Close Physical Proximity ◽  
Transcription Complexes ◽  
Factor Interactions

ABSTRACT Although biochemical and genetic methods have detected many activator-transcription factor interactions, the direct functional targets of most activators remain undetermined. For this study, photo-cross-linkers positioned within the Gal4 C-terminal acidic activating region were used to identify polypeptides in close physical proximity to Gal4 during transcription activation in vitro. Of six specifically cross-linked polypeptides, three (Tra1, Taf12, and Gal11) are subunits of four complexes (SAGA, Mediator, NuA4, and TFIID) known to play a role in gene regulation. These cross-linking targets had differential effects on activation. SAGA was critical for activation by Gal4, Gal11 contributed modestly to activation, and TFIID and NuA4 were not important for activation under our conditions. Tra1, Taf12, and Gal11 have also been identified as cross-linking targets of the Gcn4 acidic central activating region. Our results demonstrate that two unrelated acidic activators converge on the same set of functional targets.

scholarly journals Transcription Activator Interactions with Multiple SWI/SNF Subunits

2002 ◽  
Vol 22 (6) ◽  
pp. 1615-1625 ◽  
Author(s):  
Kristen E. Neely ◽  
Ahmed H. Hassan ◽  
Christine E. Brown ◽  
LeAnn Howe ◽  
Jerry L. Workman
Keyword(s):  
In Vitro Transcription ◽  
Cross Linking ◽  
Dependent Manner ◽  
Transcription Activator ◽  
Activation Domains ◽  
Label Transfer ◽  
Activation Potential ◽  
Transcriptional Stimulation

ABSTRACT We have previously shown that the yeast SWI/SNF complex stimulates in vitro transcription from chromatin templates in an ATP-dependent manner. SWI/SNF function in this regard requires the presence of an activator with which it can interact directly, linking activator recruitment of SWI/SNF to transcriptional stimulation. In this study, we determine the SWI/SNF subunits that mediate its interaction with activators. Using a photo-cross-linking label transfer strategy, we show that the Snf5, Swi1, and Swi2/Snf2 subunits are contacted by the yeast acidic activators, Gcn4 and Hap4, in the context of the intact native SWI/SNF complex. In addition, we show that the same three subunits can interact individually with acidic activation domains, indicating that each subunit contributes to binding activators. Furthermore, mutations that reduce the activation potential of these activators also diminish its interaction with each of these SWI/SNF subunits. Thus, three distinct subunits of the SWI/SNF complex contribute to its interactions with activation domains.

Polyamines are important for attachment of IEC-6 cells to extracellular matrix

1997 ◽  
Vol 273 (1) ◽  
pp. G175-G183 ◽  
Author(s):  
M. F. Santos ◽  
M. J. Viar ◽  
S. A. McCormack ◽  
L. R. Johnson
Keyword(s):  
Extracellular Matrix ◽  
Cell Migration ◽  
Cell Attachment ◽  
Specific Inhibitor ◽  
Cross Linking ◽  
Integrin Subunit ◽  
Dependent Manner ◽  
Polyamine Biosynthesis ◽  
Surface Receptors ◽  
Protein Cross Linking

The inhibition of ornithine decarboxylase, a rate-limiting enzyme of polyamine biosynthesis, with alpha-difluoromethylornithine in IEC-6 cells (small intestinal crypt cell line) reduces cell migration by 70%, inhibits protein cross-linking, and affects the cytoskeletal assembly. The current study examines the effects of intracellular polyamine depletion on attachment of IEC-6 cells to different matrices. Polyamine deficiency inhibited cell attachment to plastic, laminin, fibronectin, collagen IV, and Matrigel by different extents. Intracellular putrescine restored attachment to all matrices. The presence of a specific inhibitor of protein cross-linking also inhibited attachment to laminin in a dose-dependent manner. The inhibition of cell attachment to plastic and Matrigel was correlated with the inhibition of cell migration. Immunofluorescence studies showed that polyamines are essential for the correct expression of the integrin subunit alpha 2 but not for the expression of the alpha 1-subunit. This study demonstrates that polyamines are important for cell attachment and expression of the integrin alpha 2 beta 1, a putative receptor for collagen and laminin. The impairment of protein cross-linking and the inhibition of the expression of cell surface receptors that bind extracellular matrix (ECM) proteins may be part of the mechanism by which polyamine deficiency retards cell migration in the small intestine.

scholarly journals Stimulation of transcription factor binding and histone displacement by nucleosome assembly protein 1 and nucleoplasmin requires disruption of the histone octamer.

1995 ◽  
Vol 15 (11) ◽  
pp. 6178-6187 ◽  
Author(s):  
P P Walter ◽  
T A Owen-Hughes ◽  
J Côté ◽  
J L Workman
Keyword(s):  
Transcription Factor ◽  
Transcription Factor Binding ◽  
Nucleosome Assembly ◽  
Factor Binding ◽  
Nucleosome Assembly Protein ◽  
Histone Octamer ◽  
Nucleosomal Dna ◽  
Nucleosome Assembly Protein 1 ◽  
Histone Octamers ◽  
Stimulation Of

To investigate the mechanisms by which transcription factors invade nucleosomal DNA and replace histones at control elements, we have examined the response of the histone octamer to transcription factor binding in the presence of histone-binding proteins (i.e., nucleosome assembly factors). We found that yeast nucleosome assembly protein 1 (NAP-1) stimulated transcription factor binding and nucleosome displacement in a manner similar to that of nucleoplasmin. In addition, disruption of the histone octamer was required both for the stimulation of transcription factor binding to nucleosomal DNA and for transcription factor-induced nucleosome displacement mediated by nucleoplasmin or NAP-1. While NAP-1 and nucleoplasmin stimulated the binding of a fusion protein (GAL4-AH) to control nucleosome cores, this stimulation was lost upon covalent histone-histone cross-linking within the histone octamers. In addition, both NAP-1 and nucleoplasmin were able to mediate histone displacement upon the binding of five GAL4-AH dimers to control nucleosome cores; however, this activity was also forfeited when the histone octamers were cross-linked. These data indicate that octamer disruption is required for both stimulation of factor binding and factor-dependent histone displacement by nucleoplasmin and NAP-1. By contrast, transcription factor-induced histone transfer onto nonspecific competitor DNA did not require disruption of the histone octamer. Thus, histone displacement in this instance occurred by transfer of complete histone octamers, a mechanism distinct from that mediated by the histone-binding proteins nucleoplasmin and NAP-1.

Transglutaminases: Protein Cross-Linking Enzymes in Tissues and Body Fluids

1994 ◽  
Vol 71 (04) ◽  
pp. 402-415 ◽  
Author(s):  
Daniel Aeschlimann ◽  
Mats Paulsson
Keyword(s):  
Body Fluids ◽  
Cross Linking ◽  
Protein Cross Linking

Tridegin, a Novel Peptidic Inhibitor of Factor XIIIa from the Leech, Haementeria ghilianii, Enhances Fibrinolysis In Vitro

1997 ◽  
Vol 77 (05) ◽  
pp. 0959-0963 ◽  
Author(s):  
Lisa Seale ◽  
Sarah Finney ◽  
Roy T Sawyer ◽  
Robert B Wallis
Keyword(s):  
Potent Inhibitor ◽  
Platelet Rich Plasma ◽  
Factor Xiiia ◽  
Cross Linking ◽  
Fibrinolytic Enzymes ◽  
Small Polypeptide ◽  
Tissue Plasminogen ◽  
Protein Cross Linking

SummaryTridegin is a potent inhibitor of factor Xllla from the leech, Haementeria ghilianii, which inhibits protein cross-linking. It modifies plasmin-mediated fibrin degradation as shown by the absence of D-dimer and approximately halves the time for fibrinolysis. Plasma clots formed in the presence of Tridegin lyse more rapidly when either streptokinase, tissue plasminogen activator or hementin is added 2 h after clot formation. The effect of Tridegin is markedly increased if clots are formed from platelet-rich plasma. Platelet-rich plasma clots are lysed much more slowly by the fibrinolytic enzymes used and if Tridegin is present, the rate of lysis returns almost to that of platelet- free clots. These studies indicate the important role of platelets in conferring resistance to commonly used fibrinolytic enzymes and suggest that protein cross-linking is an important step in this effect. Moreover they indicate that Tridegin, a small polypeptide, may have potential as an adjunct to thrombolytic therapy.

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