MyoD Targets Chromatin Remodeling Complexes to the Myogenin Locus Prior to Forming a Stable DNA-Bound Complex

ABSTRACT The activation of muscle-specific gene expression requires the coordinated action of muscle regulatory proteins and chromatin-remodeling enzymes. Microarray analysis performed in the presence or absence of a dominant-negative BRG1 ATPase demonstrated that approximately one-third of MyoD-induced genes were highly dependent on SWI/SNF enzymes. To understand the mechanism of activation, we performed chromatin immunoprecipitations analyzing the myogenin promoter. We found that H4 hyperacetylation preceded Brg1 binding in a MyoD-dependent manner but that MyoD binding occurred subsequent to H4 modification and Brg1 interaction. In the absence of functional SWI/SNF enzymes, muscle regulatory proteins did not bind to the myogenin promoter, thereby providing evidence for SWI/SNF-dependent activator binding. We observed that the homeodomain factor Pbx1, which cooperates with MyoD to stimulate myogenin expression, is constitutively bound to the myogenin promoter in a SWI/SNF-independent manner, suggesting a two-step mechanism in which MyoD initially interacts indirectly with the myogenin promoter and attracts chromatin-remodeling enzymes, which then facilitate direct binding by MyoD and other regulatory proteins.

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The Drosophila trithorax group proteins BRM, ASH1 and ASH2 are subunits of distinct protein complexes

Development ◽

10.1242/dev.125.20.3955 ◽

1998 ◽

Vol 125 (20) ◽

pp. 3955-3966 ◽

Cited By ~ 26

Author(s):

O. Papoulas ◽

S.J. Beek ◽

S.L. Moseley ◽

C.M. McCallum ◽

M. Sarte ◽

...

Keyword(s):

Chromatin Remodeling ◽

Protein Complexes ◽

Dominant Negative ◽

Homeotic Genes ◽

Atpase Subunit ◽

Trithorax Group ◽

Chromatin Remodeling Complexes ◽

Trithorax Group Proteins ◽

Drosophila Embryos

The trithorax group gene brahma (brm) encodes an activator of Drosophila homeotic genes that functions as the ATPase subunit of a large protein complex. To determine if BRM physically interacts with other trithorax group proteins, we purified the BRM complex from Drosophila embryos and analyzed its subunit composition. The BRM complex contains at least seven major polypeptides. Surprisingly, the majority of the subunits of the BRM complex are not encoded by trithorax group genes. Furthermore, a screen for enhancers of a dominant-negative brm mutation identified only one trithorax group gene, moira (mor), that appears to be essential for brm function in vivo. Four of the subunits of the BRM complex are related to subunits of the yeast chromatin remodeling complexes SWI/SNF and RSC. The BRM complex is even more highly related to the human BRG1 and hBRM complexes, but lacks the subunit heterogeneity characteristic of these complexes. We present biochemical evidence for the existence of two additional complexes containing trithorax group proteins: a 2 MDa ASH1 complex and a 500 kDa ASH2 complex. These findings suggest that BRM plays a role in chromatin remodeling that is distinct from the function of most other trithorax group proteins.

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Poly(ADP-ribose)-dependent chromatin unfolding facilitates the association of DNA-binding proteins with DNA at sites of damage

Nucleic Acids Research ◽

10.1093/nar/gkz820 ◽

2019 ◽

Vol 47 (21) ◽

pp. 11250-11267 ◽

Cited By ~ 8

Author(s):

Rebecca Smith ◽

Théo Lebeaupin ◽

Szilvia Juhász ◽

Catherine Chapuis ◽

Ostiane D’Augustin ◽

...

Keyword(s):

Dna Damage ◽

Dna Binding ◽

Chromatin Remodeling ◽

Direct Interaction ◽

Dna Lesions ◽

Dependent Manner ◽

Binding Domains ◽

Damage Response ◽

Direct Binding ◽

Dnase Hypersensitivity

Abstract The addition of poly(ADP-ribose) (PAR) chains along the chromatin fiber due to PARP1 activity regulates the recruitment of multiple factors to sites of DNA damage. In this manuscript, we investigated how, besides direct binding to PAR, early chromatin unfolding events controlled by PAR signaling contribute to recruitment to DNA lesions. We observed that different DNA-binding, but not histone-binding, domains accumulate at damaged chromatin in a PAR-dependent manner, and that this recruitment correlates with their affinity for DNA. Our findings indicate that this recruitment is promoted by early PAR-dependent chromatin remodeling rather than direct interaction with PAR. Moreover, recruitment is not the consequence of reduced molecular crowding at unfolded damaged chromatin but instead originates from facilitated binding to more exposed DNA. These findings are further substantiated by the observation that PAR-dependent chromatin remodeling at DNA lesions underlies increased DNAse hypersensitivity. Finally, the relevance of this new mode of PAR-dependent recruitment to DNA lesions is demonstrated by the observation that reducing the affinity for DNA of both CHD4 and HP1α, two proteins shown to be involved in the DNA-damage response, strongly impairs their recruitment to DNA lesions.

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Octamer Transfer and Creation of Stably Remodeled Nucleosomes by Human SWI-SNF and Its Isolated ATPases

Molecular and Cellular Biology ◽

10.1128/mcb.20.17.6380-6389.2000 ◽

2000 ◽

Vol 20 (17) ◽

pp. 6380-6389 ◽

Cited By ~ 74

Author(s):

Michael L. Phelan ◽

Gavin R. Schnitzler ◽

Robert E. Kingston

Keyword(s):

Chromatin Remodeling ◽

Dependent Manner ◽

Chromatin Remodeling Complexes ◽

Atpase Subunits ◽

Histone Octamers

ABSTRACT Chromatin remodeling complexes help regulate the structure of chromatin to facilitate transcription. The multisubunit human (h) SWI-SNF complex has been shown to remodel mono- and polynucleosome templates in an ATP-dependent manner. The isolated hSWI-SNF ATPase subunits BRG1 and hBRM also have these activities. The intact complex has been shown to produce a stable remodeled dimer of mononucleosomes as a product. Here we show that the hSWI-SNF ATPases alone can also produce this product. In addition, we show that hSWI-SNF and its ATPases have the ability to transfer histone octamers from donor nucleosomes to acceptor DNA. These two reactions are characterized and compared. Our results are consistent with both products of SWI-SNF action being formed as alternative outcomes of a single remodeling mechanism. The ability of the isolated ATPase subunits to catalyze these reactions suggests that these subunits play a key role in determining the mechanistic capabilities of the SWI-SNF family of remodeling complexes.

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Neuronal Activity-Induced BRG1 Phosphorylation Regulates Enhancer Activation

10.1101/2020.09.01.278101 ◽

2020 ◽

Author(s):

Bongwoo Kim ◽

Yi Luo ◽

Xiaoming Zhan ◽

Zilai Zhang ◽

Xuanming Shi ◽

...

Keyword(s):

Rna Polymerase Ii ◽

Chromatin Remodeling ◽

Neuronal Activity ◽

Phosphorylation Site ◽

Serine Phosphorylation ◽

Dependent Manner ◽

Enhancer Rna ◽

Induce Activity ◽

Chromatin Remodeling Complexes ◽

Activity Dependent

SUMMARYNeuronal activity-induced enhancers drive the gene induction in response to stimulation. Here, we demonstrate that BRG1, the core subunit of SWI/SNF-like BAF ATP-dependent chromatin remodeling complexes, regulates neuronal activity-induced enhancers. Upon stimulation, BRG1 is recruited to enhancers in an H3K27Ac-dependent manner. BRG1 regulates enhancer basal activities and inducibility by affecting cohesin binding, enhancer-promoter looping, RNA polymerase II recruitment, and enhancer RNA expression. Furthermore, we identified a serine phosphorylation site in BRG1 that is induced by neuronal activities and is sensitive to CaMKII inhibition. BRG1 phosphorylation affects its interaction with several transcription co-factors, possibly modulating BRG1 mediated transcription outcomes. Using mice with knock-in mutations, we showed that non-phosphorylatable BRG1 fails to efficiently induce activity-dependent genes, whereas phosphomimic BRG1 increases the enhancer activities and inducibility. These mutant mice displayed anxiety-like phenotypes and altered responses to stress. Therefore, our data reveal a mechanism connecting neuronal signaling to enhancer activities through BRG1 phosphorylation.

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Mannheimia haemolytica Leukotoxin Binds to Lipid Rafts in Bovine Lymphoblastoid Cells and Is Internalized in a Dynamin-2- and Clathrin-Dependent Manner

Infection and Immunity ◽

10.1128/iai.00534-07 ◽

2007 ◽

Vol 75 (10) ◽

pp. 4719-4727 ◽

Cited By ~ 24

Author(s):

Dhammika N. Atapattu ◽

Charles J. Czuprynski

Keyword(s):

Lipid Rafts ◽

Actin Polymerization ◽

Bacterial Pathogen ◽

Dominant Negative ◽

Mannheimia Haemolytica ◽

Complex Nature ◽

Dependent Manner ◽

Coated Pits ◽

Independent Manner ◽

Dynamin 2

ABSTRACT Mannheimia haemolytica is the principal bacterial pathogen of the bovine respiratory disease complex. Its most important virulence factor is a leukotoxin (LKT), which is a member of the RTX family of exotoxins produced by many gram-negative bacteria. Previous studies demonstrated that LKT binds to the β2-integrin LFA-1 (CD11a/CD18) on bovine leukocytes, resulting in cell death. In this study, we demonstrated that depletion of lipid rafts significantly decreases LKT-induced bovine lymphoblastoid cell (BL-3) death. After binding to BL-3 cells, some of the LKT relocated to lipid rafts in an LFA-1-independent manner. We hypothesized that after binding to LFA-1 on BL-3 cells, LKT moves to lipid rafts and clathrin-coated pits via a dynamic process that results in LKT internalization and cytotoxicity. Knocking down dynamin-2 by small interfering RNA reduced both LKT internalization and cytotoxicity. Similarly, expression of dominant negative Eps15 protein expression, which is required for clathrin coat formation, reduced LKT internalization and LKT-mediated cytotoxicity to BL-3 cells. Finally, we demonstrated that inhibiting actin polymerization reduced both LKT internalization and LKT-mediated cytotoxicity. These results suggest that both lipid rafts and clathrin-mediated mechanisms are important for LKT internalization and cytotoxicity in BL-3 cells and illustrate the complex nature of LKT internalization by the cytoskeletal network.

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AtINO80 represses photomorphogenesis by modulating nucleosome density and H2A.Z incorporation in light-related genes

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2001976117 ◽

2020 ◽

Vol 117 (52) ◽

pp. 33679-33688

Author(s):

Chuanwei Yang ◽

Liufan Yin ◽

Famin Xie ◽

Mengmeng Ma ◽

Sha Huang ◽

...

Keyword(s):

Chromatin Remodeling ◽

Transcriptional Control ◽

Developmental Process ◽

Morphological Changes ◽

Dependent Manner ◽

Transcriptional Reprogramming ◽

Genome Wide ◽

Nucleosome Density ◽

Induced Genes ◽

Fine Tune

Photomorphogenesis is a critical developmental process bridging light-regulated transcriptional reprogramming with morphological changes in organisms. Strikingly, the chromatin-based transcriptional control of photomorphogenesis remains poorly understood. Here, we show that the Arabidopsis (Arabidopsis thaliana) ortholog of ATP-dependent chromatin-remodeling factor AtINO80 represses plant photomorphogenesis. Loss of AtINO80 inhibited hypocotyl cell elongation and caused anthocyanin accumulation. Both light-induced genes and dark-induced genes were affected in the atino80 mutant. Genome-wide occupancy of the H2A.Z histone variant and levels of histone H3 were reduced in atino80. In particular, AtINO80 bound the gene body of ELONGATED HYPOCOTYL 5 (HY5), resulting in lower chromatin incorporations of H2A.Z and H3 at HY5 in atino80. Genetic analysis revealed that AtINO80 acts in a phytochrome B- and HY5-dependent manner in the regulation of photomorphogenesis. Together, our study elucidates a mechanism wherein AtINO80 modulates nucleosome density and H2A.Z incorporation and represses the transcription of light-related genes, such as HY5, to fine tune plant photomorphogenesis.

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Chromatin Remodeling Complexes Interact Dynamically with a Glucocorticoid Receptor–regulated Promoter

Molecular Biology of the Cell ◽

10.1091/mbc.e08-02-0123 ◽

2008 ◽

Vol 19 (8) ◽

pp. 3308-3322 ◽

Cited By ~ 67

Author(s):

Thomas A. Johnson ◽

Cem Elbi ◽

Bhavin S. Parekh ◽

Gordon L. Hager ◽

Sam John

Keyword(s):

Rna Polymerase Ii ◽

Chromatin Remodeling ◽

Transcriptional Activation ◽

Tandem Repeats ◽

Inducible Promoter ◽

Kinetic Properties ◽

Dependent Manner ◽

Chromatin Remodeling Complexes ◽

Mmtv Promoter

Brahma (BRM) and Brahma-related gene 1 (BRG1) are the ATP-dependent catalytic subunits of the SWI/SNF family of chromatin-remodeling complexes. These complexes are involved in essential processes such as cell cycle, growth, differentiation, and cancer. Using imaging approaches in a cell line that harbors tandem repeats of stably integrated copies of the steroid responsive MMTV-LTR (mouse mammary tumor virus–long terminal repeat), we show that BRG1 and BRM are recruited to the MMTV promoter in a hormone-dependent manner. The recruitment of BRG1 and BRM resulted in chromatin remodeling and decondensation of the MMTV repeat as demonstrated by an increase in the restriction enzyme accessibility and in the size of DNA fluorescence in situ hybridization (FISH) signals. This chromatin remodeling event was concomitant with an increased occupancy of RNA polymerase II and transcriptional activation at the MMTV promoter. The expression of ATPase-deficient forms of BRG1 (BRG1-K-R) or BRM (BRM-K-R) inhibited the remodeling of local and higher order MMTV chromatin structure and resulted in the attenuation of transcription. In vivo photobleaching experiments provided direct evidence that BRG1, BRG1-K-R, and BRM chromatin-remodeling complexes have distinct kinetic properties on the MMTV array, and they dynamically associate with and dissociate from MMTV chromatin in a manner dependent on hormone and a functional ATPase domain. Our data provide a kinetic and mechanistic basis for the BRG1 and BRM chromatin-remodeling complexes in regulating gene expression at a steroid hormone inducible promoter.

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Gas1 is a receptor for sonic hedgehog to repel enteric axons

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1418629112 ◽

2014 ◽

Vol 112 (1) ◽

pp. E73-E80 ◽

Cited By ~ 29

Author(s):

Shiying Jin ◽

David C. Martinelli ◽

Xiaobin Zheng ◽

Marc Tessier-Lavigne ◽

Chen-Ming Fan

Keyword(s):

Sonic Hedgehog ◽

Smooth Muscles ◽

Axon Growth ◽

Dominant Negative ◽

Enteric Neurons ◽

Specific Gene ◽

Dependent Manner ◽

Central Projections ◽

Gut Epithelium

The myenteric plexus of the enteric nervous system controls the movement of smooth muscles in the gastrointestinal system. They extend their axons between two peripheral smooth muscle layers to form a tubular meshwork arborizing the gut wall. How a tubular axonal meshwork becomes established without invading centrally toward the gut epithelium has not been addressed. We provide evidence here that sonic hedgehog (Shh) secreted from the gut epithelium prevents central projections of enteric axons, thereby forcing their peripheral tubular distribution. Exclusion of enteric central projections by Shh requires its binding partner growth arrest specific gene 1 (Gas1) and its signaling component smoothened (Smo) in enteric neurons. Using enteric neurons differentiated from neurospheres in vitro, we show that enteric axon growth is not inhibited by Shh. Rather, when Shh is presented as a point source, enteric axons turn away from it in a Gas1-dependent manner. Of the Gαi proteins that can couple with Smo, G protein α Z (Gnaz) is found in enteric axons. Knockdown and dominant negative inhibition of Gnaz dampen the axon-repulsive response to Shh, and Gnaz mutant intestines contain centrally projected enteric axons. Together, our data uncover a previously unsuspected mechanism underlying development of centrifugal tubular organization and identify a previously unidentified effector of Shh in axon guidance.

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