Regulation of Egr1 Target Genes by the Nurd Chromatin Remodeling Complex

ABSTRACT The gene encoding the SNF5/Ini1 core subunit of the SWI/SNF chromatin remodeling complex is a tumor suppressor in humans and mice, with an essential role in early embryonic development. To investigate further the function of this gene, we have generated a Cre/lox-conditional mouse line. We demonstrate that Snf5 deletion in primary fibroblasts impairs cell proliferation and survival without the expected derepression of most retinoblastoma protein-controlled, E2F-responsive genes. Furthermore, Snf5-deficient cells are hypersensitive to genotoxic stress, display increased aberrant mitotic features, and accumulate phosphorylated p53, leading to elevated expression of a specific subset of p53 target genes, suggesting a role for Snf5 in the DNA damage response. p53 inactivation does not rescue the proliferation defect caused by Snf5 deficiency but reduces apoptosis and strongly accelerates tumor formation in Snf5-heterozygous mice.

Download Full-text

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

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1800930115 ◽

2018 ◽

Vol 115 (32) ◽

pp. 8173-8178 ◽

Cited By ~ 2

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.

Download Full-text

Crucial Roles for Interactions between MLL3/4 and INI1 in Nuclear Receptor Transactivation

Molecular Endocrinology ◽

10.1210/me.2008-0455 ◽

2009 ◽

Vol 23 (5) ◽

pp. 610-619 ◽

Cited By ~ 36

Author(s):

Seunghee Lee ◽

Dae-Hwan Kim ◽

Young Hwa Goo ◽

Young Chul Lee ◽

Soo-Kyung Lee ◽

...

Keyword(s):

Nuclear Receptor ◽

Chromatin Remodeling ◽

Target Genes ◽

Mutational Analysis ◽

Specific Protein ◽

Transcriptional Coactivator ◽

Set Domain ◽

Protein Protein Interaction ◽

Terminal Set ◽

Chromatin Remodeling Complex

Abstract Nuclear receptor (NR) transactivation involves multiple coactivators, and the molecular basis for how these are functionally integrated needs to be determined to fully understand the NR action. Activating signal cointegrator-2 (ASC-2), a transcriptional coactivator of many NRs and transcription factors, forms a steady-state complex, ASCOM (for ASC-2 complex), which contains histone H3-lysine-4 (H3K4) methyltransferase MLL3 or its paralog MLL4. Here, we show that ASCOM requires a functional cross talk with the ATPase-dependent chromatin remodeling complex Swi/Snf for efficient NR transactivation. Our results reveal that ASCOM and Swi/Snf are tightly colocalized in the nucleus and that ASCOM and Swi/Snf promote each other’s binding to NR target genes. We further show that the C-terminal SET domain of MLL3 and MLL4 directly interacts with INI1, an integral subunit of Swi/Snf. Our mutational analysis demonstrates that this interaction underlies the mutual facilitation of ASCOM and Swi/Snf recruitment to NR target genes. Importantly, this study uncovers a specific protein-protein interaction as a novel venue to couple two distinct enzymatic coactivator complexes during NR transactivation.

Download Full-text

SWI/SNF chromatin remodeling controls Notch-responsive enhancer accessibility

10.1101/399501 ◽

2018 ◽

Author(s):

Zoe Pillidge ◽

Sarah J Bray

Keyword(s):

Notch Signaling ◽

Cell Fate ◽

Chromatin Remodeling ◽

Target Genes ◽

Transcriptional Response ◽

Histone Chaperones ◽

Chromatin Remodelers ◽

Cell Fate Decisions ◽

Chromatin Remodeling Complex ◽

Brahma Complex

AbstractNotch signaling plays a key role in many cell fate decisions during development by directing different gene expression programs via the transcription factor CSL, known as Su(H) in Drosophila. Which target genes are responsive to Notch signaling is influenced by the chromatin state of enhancers, yet how this is regulated is not fully known. Detecting an increase in the histone variant H3.3 in response to Notch signaling, we tested which chromatin remodelers or histone chaperones were required for the changes in enhancer accessibility to Su(H) binding. This revealed a crucial role for the Brahma SWI/SNF chromatin remodeling complex in conferring enhancer accessibility and enabling the transcriptional response. The Notch-responsive regions had high levels of nucleosome turnover which were dependent on the Brahma complex, increased with Notch signaling and primarily involved histone H3.3. Together these results highlight the importance of SWI/SNF-mediated nucleosome turnover in rendering enhancers responsive to Notch.

Download Full-text

Cdx2 Regulates Gene Expression through Recruitment of Brg1-associated Switch-Sucrose Non-fermentable (SWI-SNF) Chromatin Remodeling Activity

Journal of Biological Chemistry ◽

10.1074/jbc.m116.752774 ◽

2017 ◽

Vol 292 (8) ◽

pp. 3389-3399 ◽

Cited By ~ 6

Author(s):

Thinh T. Nguyen ◽

Joanne G. A. Savory ◽

Travis Brooke-Bisschop ◽

Randy Ringuette ◽

Tanya Foley ◽

...

Keyword(s):

Gene Expression ◽

Transcriptional Regulation ◽

Transcription Factors ◽

Chromatin Remodeling ◽

Genomic Dna ◽

Direct Contact ◽

Target Gene ◽

Target Genes ◽

Limited Ability ◽

Chromatin Remodeling Complex

The packaging of genomic DNA into nucleosomes creates a barrier to transcription that can be relieved through ATP-dependent chromatin remodeling via complexes such as the switch-sucrose non-fermentable (SWI-SNF) chromatin remodeling complex. The SWI-SNF complex remodels chromatin via conformational or positional changes of nucleosomes, thereby altering the access of transcriptional machinery to target genes. The SWI-SNF complex has limited ability to bind to sequence-specific elements, and, therefore, its recruitment to target loci is believed to require interaction with DNA-associated transcription factors. The Cdx family of homeodomain transcript ion factors (Cdx1, Cdx2, and Cdx4) are essential for a number of developmental programs in the mouse. Cdx1 and Cdx2 also regulate intestinal homeostasis throughout life. Although a number of Cdx target genes have been identified, the basis by which Cdx members impact their transcription is poorly understood. We have found that Cdx members interact with the SWI-SNF complex and make direct contact with Brg1, a catalytic member of SWI-SNF. Both Cdx2 and Brg1 co-occupy a number of Cdx target genes, and both factors are necessary for transcriptional regulation of such targets. Finally, Cdx2 and Brg1 occupancy occurs coincident with chromatin remodeling at some of these loci. Taken together, our findings suggest that Cdx transcription factors regulate target gene expression, in part, through recruitment of Brg1-associated SWI-SNF chromatin remodeling activity.

Download Full-text

Osa associates with the Brahma chromatin remodeling complex and promotes the activation of some target genes

The EMBO Journal ◽

10.1093/emboj/18.24.7029 ◽

1999 ◽

Vol 18 (24) ◽

pp. 7029-7040 ◽

Cited By ~ 101

Author(s):

R. T. Collins

Keyword(s):

Chromatin Remodeling ◽

Target Genes ◽

Chromatin Remodeling Complex

Download Full-text

Screening for Inhibitors of an Essential Chromatin Remodeler in Mouse Embryonic Stem Cells by Monitoring Transcriptional Regulation

CrossRef Listing of Deleted DOIs ◽

10.1177/1087057112455060 ◽

2012 ◽

Vol 17 (9) ◽

pp. 1221-1230 ◽

Cited By ~ 19

Author(s):

Emily C. Dykhuizen ◽

Leigh C. Carmody ◽

Nicola Tolliday ◽

Gerald R. Crabtree ◽

Michelle A. J. Palmer

Keyword(s):

Chromatin Remodeling ◽

Protein Interactions ◽

Target Genes ◽

Es Cells ◽

Embryonic Stem ◽

Diversity Oriented Synthesis ◽

Qrt Pcr ◽

Chromatin Remodeling Complex ◽

Successful Approach ◽

Polymerase Chain

The SWI/SNF-like adenosine triphosphate (ATP)–dependent chromatin remodeling complex, esBAF, is both necessary and, in some contexts, sufficient to induce the pluripotent state. Furthermore, mutations in various BAF subunits are associated with cancer. Little is known regarding the precise mechanism(s) by which this complex exerts its activities. Thus, it is unclear which protein interactions would be important to disrupt to isolate a relevant readout of mechanism. To address this, we developed a gene expression–based assay to identify inhibitors of the native esBAF complex. Specifically, a quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) assay was developed in mouse embryonic stem (ES) cells to monitor expression of Bmi1, a developmentally important gene repressed by the esBAF complex. The assay was miniaturized to a 384-well format and used to screen a diverse collection of compounds, including novel products of diversity-oriented synthesis (DOS). Confirmed hits were validated using a knock-in ES cell reporter line in which luciferase is inserted into the Bmi1 locus. Several of the validated hits regulate a panel of target genes in a manner similar to the BAF chromatin-remodeling complex. Together these data indicate that expression-based screening using qRT-PCR is a successful approach to identify compounds targeting the regulation of key developmental genes in ES cells.

Download Full-text

MUC1-C activates the PBAF chromatin remodeling complex in integrating redox balance with progression of human prostate cancer stem cells

Oncogene ◽

10.1038/s41388-021-01899-y ◽

2021 ◽

Author(s):

Masayuki Hagiwara ◽

Atsushi Fushimi ◽

Nami Yamashita ◽

Atrayee Bhattacharya ◽

Hasan Rajabi ◽

...

Keyword(s):

Prostate Cancer ◽

Chromatin Remodeling ◽

Target Genes ◽

Redox Balance ◽

Chromatin Accessibility ◽

Pentose Phosphate ◽

Antioxidant Genes ◽

Chromatin Remodeling Complex ◽

Prostate Cancer Stem Cells ◽

Oncogenic Protein

AbstractThe polybromo-associated PBAF (SWI/SNF) chromatin remodeling complex, which includes PBRM1, ARID2, and BRD7, regulates cell differentiation and genomic integrity. MUC1-C is an oncogenic protein that drives lineage plasticity in prostate cancer (PC) progression. The present work demonstrates that MUC1-C induces PBRM1, ARID2, and BRD7 expression by the previously unrecognized E2F1-mediated activation of their respective promoters. The functional significance of the MUC1-C→PBAF pathway is supported by demonstrating involvement of MUC1-C in associating with nuclear PBAF and driving the NRF2 antioxidant gene transcriptome in PC cells. Mechanistically, MUC1-C forms a complex with NRF2 and PBRM1 on the NRF2 target SLC7A11 gene that encodes the xCT cystine-glutamate antiporter, increases chromatin accessibility and induces SLC7A11/xCT expression. We also show that MUC1-C and PBRM1 are necessary for induction of other NRF2 target genes, including G6PD and PGD that regulate the pentose phosphate pathway. Our results further demonstrate that MUC1-C integrates activation of PBRM1 with the regulation of antioxidant genes, ROS levels, pluripotency factor expression and the cancer stem cell (CSC) state. These findings reveal a role for MUC1-C in regulating PBAF, redox balance and lineage plasticity of PC CSC progression. Our findings also uncover involvement of MUC1-C in integrating the PBAF and BAF pathways in cancer.

Download Full-text

Combined genomic and proteomic approaches reveal DNA binding sites and interaction partners of TBX2 in the developing lung

Respiratory Research ◽

10.1186/s12931-021-01679-y ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Timo H. Lüdtke ◽

Irina Wojahn ◽

Marc-Jens Kleppa ◽

Jasper Schierstaedt ◽

Vincent M. Christoffels ◽

...

Keyword(s):

Transcription Factor ◽

Dna Binding ◽

Chromatin Remodeling ◽

Binding Sites ◽

Target Genes ◽

Branching Morphogenesis ◽

Hmg Box ◽

Chromatin Remodeling Complex ◽

Dna Binding Sites ◽

Interaction Partners

Abstract Background Tbx2 encodes a transcriptional repressor implicated in the development of numerous organs in mouse. During lung development TBX2 maintains the proliferation of mesenchymal progenitors, and hence, epithelial proliferation and branching morphogenesis. The pro-proliferative function was traced to direct repression of the cell-cycle inhibitor genes Cdkn1a and Cdkn1b, as well as of genes encoding WNT antagonists, Frzb and Shisa3, to increase pro-proliferative WNT signaling. Despite these important molecular insights, we still lack knowledge of the DNA occupancy of TBX2 in the genome, and of the protein interaction partners involved in transcriptional repression of target genes. Methods We used chromatin immunoprecipitation (ChIP)-sequencing and expression analyses to identify genomic DNA-binding sites and transcription units directly regulated by TBX2 in the developing lung. Moreover, we purified TBX2 containing protein complexes from embryonic lung tissue and identified potential interaction partners by subsequent liquid chromatography/mass spectrometry. The interaction with candidate proteins was validated by immunofluorescence, proximity ligation and individual co-immunoprecipitation analyses. Results We identified Il33 and Ccn4 as additional direct target genes of TBX2 in the pulmonary mesenchyme. Analyzing TBX2 occupancy data unveiled the enrichment of five consensus sequences, three of which match T-box binding elements. The remaining two correspond to a high mobility group (HMG)-box and a homeobox consensus sequence motif. We found and validated binding of TBX2 to the HMG-box transcription factor HMGB2 and the homeobox transcription factor PBX1, to the heterochromatin protein CBX3, and to various members of the nucleosome remodeling and deacetylase (NuRD) chromatin remodeling complex including HDAC1, HDAC2 and CHD4. Conclusion Our data suggest that TBX2 interacts with homeobox and HMG-box transcription factors as well as with the NuRD chromatin remodeling complex to repress transcription of anti-proliferative genes in the pulmonary mesenchyme.

Download Full-text