Chromatin accessibility changes after BAF complex disruption in neuroblastoma cells by ATAC-Seq
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE202306 | GEO | 2022/11/01
REPOSITORIES: GEO
Similar Datasets
Project description:In order to determine the transcriptomic network under the control of BAF chromatin remodeling complex in neuroblastoma cells, we performed RNA-Seq analysis on a neuroblastoma cell lines to detect those transcriptionally modulated genes after the disruption of this complex through silencing of its key structural subunits ARID1A and ARID1B.
2022-11-01 | GSE202231 | GEO
Project description:The BAF complex modulates chromatin accessibility. Specific BAF configurations have functional consequences, and subunit switches are essential for cell differentiation. ARID1B and its paralog ARID1A encode for mutually exclusive BAF subunits. De novo ARID1B haploinsufficient mutations cause a neurodevelopmental disorder spectrum, including Coffin-Siris syndrome, which is characterized by neurological and craniofacial features. Here, we reprogrammed ARID1B+/- Coffin-Siris patient-derived skin fibroblasts into iPSCs, and modeled cranial neural crest cell (CNCC) formation. We discovered that ARID1B is active only during the first stage of this process, coinciding with neuroectoderm specification, where it is part of a lineage-specific BAF configuration (ARID1B-BAF), including SMARCA4, and nine additional subunits. ARID1B-BAF acts as a gate-keeper, ensuring exit from pluripotency and lineage commitment, by attenuating NANOG, SOX2 and the thousands of enhancers directly regulated by these two pluripotency factors at the iPSC stage. In iPSCs, these enhancers are maintained active by an ARID1A-containing BAF. At the onset of differentiation, cells transition from ARID1A-BAF to ARID1B-BAF, eliciting attenuation of the NANOG/SOX2 networks, and triggering pluripotency exit. Coffin-Siris patient cells fail to perform the ARID1A/ARID1B switch, and maintain ARID1A-BAF at pluripotency enhancers throughout all stages of CNCC formation. This leads to a persistent and aberrant SOX2 and NANOG activity, which impairs CNCC formation. In fact, despite showing the typical neural crest signature (TFAP2A+, SOX9+), the ARID1B-haploinsufficient CNCCs are also NANOG-positive, in stark contrast with the ARID1B-wt CNCCs, which are NANOG-negative. These findings suggest a connection between ARID1B mutations, neuroectoderm formation, and a pathogenic mechanism for Coffin-Siris syndrome.
2021-10-12 | PXD028557 | Pride
Project description:RNA-Seq analysis of SK-N-BE(2) neuroblastoma cells after ARID1A and ARID1B silencing for BAF complex disruption
| PRJNA835096 | ENA
Project description:De-novo ARID1B haploinsufficient mutations cause many developmental disorders characterized by neurological and craniofacial phenotypes, including Coffin-Siris Syndrome. ARID1B and its paralog ARID1A encode for mutually exclusive subunits of the BAF chromatin remodeler, yet their role in cell-fate determination is poorly understood. We discovered a novel neural crest configuration of the BAF complex (ARID1B-BAF), which includes ARID1B, SMARCA4, and eight additional subunits. The ARID1B-BAF regulates lineage commitment upon differentiation cues through attenuation of pluripotency enhancers of the SOX2 network. Consistently, the ARID1B-BAF interacts with SALL4, which is known to have repressing abilities during lineage commitment. In iPSCs, pluripotency enhancers are maintained in active state by cooperation between the pioneer activity of SOX2 and the ARID1A-containing BAF. At the onset of differentiation, ARID1B-BAF replaces ARID1A-BAF at these enhancers, eliciting chromatin repression and coordinating the exit from pluripotency. Coffin-Siris patient cells fail to perform the ARID1A/ARID1B switch, and maintain ARID1A-BAF at the pluripotency enhancers throughout CNCC differentiation. This correlates with aberrant SOX2 binding at the pluripotency enhancers, and failure to reposition SOX2 at the developmental enhancers. SOX2 dysregulation promotes upregulation of the NANOG regulatory network, impairing CNCC differentiation. Intriguingly, the patient with the most extreme molecular phenotype is also affected by a more severe version of the syndrome. These findings have significant biomedical implications, since they suggest a direct connection between ARID1B mutations and developmental disorders.
2021-09-22 | GSE169654 | GEO
Project description:The BAF chromatin remodeler regulates lineage commitment including cranial neural crest cell (CNCC) specification. BAF subunit mutations cause Coffin-Siris Syndrome (CSS), a congenital disorder characterized by distinct craniofacial features and intellectual disability. Approximately 50% of CSS patients carry mutations in one of the mutually exclusive BAF subunits, ARID1A/ARID1B. While Arid1a deletion in mouse neural crest causes severe craniofacial phenotypes, little is known about the role of ARID1A in CNCC specification. Using CSS patient-derived ARID1A+/- iPSCs to model CNCC specification, we discovered that ARID1A-haploinsufficency impairs epithelial to mesenchymal transition (EMT), a process necessary for CNCC delamination and migration from the neural tube. Furthermore, wild-type ARID1A-BAF regulates enhancers associated with EMT genes. ARID1A-BAF binding at these enhancers is impaired in heterozygotes, while binding at promoters is unaffected. At the sequence level, these EMT enhancers contain binding motifs for ZIC2, and ZIC2 binding at these sites is ARID1A-dependent. When excluded from EMT enhancers, ZIC2 relocates to neuronal enhancers, triggering aberrant neuronal gene activation. In mice, deletion of Zic2 impairs NCC delamination, while ZIC2 overexpression in chick embryos at pre-migratory neural crest stages elicits abnormal cell delamination from the neural tube. These findings reveal a novel ARID1A-ZIC2 axis essential for EMT and CNCC delamination.
2024-07-23 | GSE261846 | GEO
Project description:Global CRISPR screens provide an unparalleled, longer-term experimental approach for the identification of essential genes in drug resistance. We used an ~18,000 gene deletion screen to discover ARID1A and other BAF complex components as the most critical factors required for response to two classes of Estrogen Receptor (ER) antagonists, namely ER degraders and Selective Estrogen Receptor Modulators (SERMs). Unexpectedly, ARID1A was also the top candidate for response to the BET inhibitor JQ1, but in the opposite direction, where loss of ARID1A sensitised breast cancer cells to BET inhibition. We show that ARIDA binds chromatin at ER cis-regulatory elements and can physically associate with ER in model systems and primary tumour samples. ARID1A binding to ER enhancer elements, can occur in the absence of ER, suggesting that its repressive activity occurs in an enhancer-specific, but ER-independent manner. Specific targeting of ARID1A validated the CRISPR screen and shows that depletion of BAF activity, does not result in redundancy from P-BAF, the other ATP-dependent chromatin remodelling complex, but instead results in loss of HDAC1 binding, increased Histone 4 lysine acetylation and subsequent BRD4-driven growth. ARID1A and the BAF complex therefore function as a critical mechanism of antiestrogen activity and mutation or depletion in BAF activity drives a BRD4-mediated proliferative program that is refractory to ER targeted agents. Since ARID1A is mutated in a subset of treatment-resistant disease, these findings provide mechanistic insight and treatment strategies for patients, based on BAF complex fidelity status.
2019-10-30 | GSE123285 | GEO
Project description:Global CRISPR screens provide an unparalleled, longer-term experimental approach for the identification of essential genes in drug resistance. We used an ~18,000 gene deletion screen to discover ARID1A and other BAF complex components as the most critical factors required for response to two classes of Estrogen Receptor (ER) antagonists, namely ER degraders and Selective Estrogen Receptor Modulators (SERMs). Unexpectedly, ARID1A was also the top candidate for response to the BET inhibitor JQ1, but in the opposite direction, where loss of ARID1A sensitised breast cancer cells to BET inhibition. We show that ARIDA binds chromatin at ER cis-regulatory elements and can physically associate with ER in model systems and primary tumour samples. ARID1A binding to ER enhancer elements, can occur in the absence of ER, suggesting that its repressive activity occurs in an enhancer-specific, but ER-independent manner. Specific targeting of ARID1A validated the CRISPR screen and shows that depletion of BAF activity, does not result in redundancy from P-BAF, the other ATP-dependent chromatin remodelling complex, but instead results in loss of HDAC1 binding, increased Histone 4 lysine acetylation and subsequent BRD4-driven growth. ARID1A and the BAF complex therefore function as a critical mechanism of antiestrogen activity and mutation or depletion in BAF activity drives a BRD4-mediated proliferative program that is refractory to ER targeted agents. Since ARID1A is mutated in a subset of treatment-resistant disease, these findings provide mechanistic insight and treatment strategies for patients, based on BAF complex fidelity status.
2019-10-30 | GSE134270 | GEO
Project description:Global CRISPR screens provide an unparalleled, longer-term experimental approach for the identification of essential genes in drug resistance. We used an ~18,000 gene deletion screen to discover ARID1A and other BAF complex components as the most critical factors required for response to two classes of Estrogen Receptor (ER) antagonists, namely ER degraders and Selective Estrogen Receptor Modulators (SERMs). Unexpectedly, ARID1A was also the top candidate for response to the BET inhibitor JQ1, but in the opposite direction, where loss of ARID1A sensitised breast cancer cells to BET inhibition. We show that ARIDA binds chromatin at ER cis-regulatory elements and can physically associate with ER in model systems and primary tumour samples. ARID1A binding to ER enhancer elements, can occur in the absence of ER, suggesting that its repressive activity occurs in an enhancer-specific, but ER-independent manner. Specific targeting of ARID1A validated the CRISPR screen and shows that depletion of BAF activity, does not result in redundancy from P-BAF, the other ATP-dependent chromatin remodelling complex, but instead results in loss of HDAC1 binding, increased Histone 4 lysine acetylation and subsequent BRD4-driven growth. ARID1A and the BAF complex therefore function as a critical mechanism of antiestrogen activity and mutation or depletion in BAF activity drives a BRD4-mediated proliferative program that is refractory to ER targeted agents. Since ARID1A is mutated in a subset of treatment-resistant disease, these findings provide mechanistic insight and treatment strategies for patients, based on BAF complex fidelity status.
2019-10-30 | GSE123284 | GEO
Project description:Global CRISPR screens provide an unparalleled, longer-term experimental approach for the identification of essential genes in drug resistance. We used an ~18,000 gene deletion screen to discover ARID1A and other BAF complex components as the most critical factors required for response to two classes of Estrogen Receptor (ER) antagonists, namely ER degraders and Selective Estrogen Receptor Modulators (SERMs). Unexpectedly, ARID1A was also the top candidate for response to the BET inhibitor JQ1, but in the opposite direction, where loss of ARID1A sensitised breast cancer cells to BET inhibition. We show that ARIDA binds chromatin at ER cis-regulatory elements and can physically associate with ER in model systems and primary tumour samples. ARID1A binding to ER enhancer elements, can occur in the absence of ER, suggesting that its repressive activity occurs in an enhancer-specific, but ER-independent manner. Specific targeting of ARID1A validated the CRISPR screen and shows that depletion of BAF activity, does not result in redundancy from P-BAF, the other ATP-dependent chromatin remodelling complex, but instead results in loss of HDAC1 binding, increased Histone 4 lysine acetylation and subsequent BRD4-driven growth. ARID1A and the BAF complex therefore function as a critical mechanism of antiestrogen activity and mutation or depletion in BAF activity drives a BRD4-mediated proliferative program that is refractory to ER targeted agents. Since ARID1A is mutated in a subset of treatment-resistant disease, these findings provide mechanistic insight and treatment strategies for patients, based on BAF complex fidelity status.
2019-10-30 | GSE123283 | GEO
Project description:Chromatin accessibility changes after BAF complex disruption in neuroblastoma cells by ATAC-Seq
| PRJNA835427 | ENA