Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA238942 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Histone H3K4 methylation has been linked to transcriptional activation. JARID1A (also known as RBP2 or KDM5A), a member of the JARID1 protein family, is an H3K4 demethylase, previously implicated in the regulation of transcription and differentiation. Here we show that JARID1A is physically and functionally associated with two histone deacetylase complexes. Immunoaffinity purification of JARID1A confirmed a previously described association with the SIN3B-containing HDAC complex, and revealed an association with the nucleosome remodeling and deacetylase (NuRD) complex. Sucrose density gradient and sequential immunoprecipitation analyses further confirmed the stable association of JARID1A with these two HDAC complexes. JARID1A depletion led to changes in the expression of hundreds of genes, two-thirds of which were also controlled by CHD4, the NuRD catalytic subunit. Gene ontology analysis confirmed that the genes commonly regulated by both JARID1A and CHD4 were categorized as developmentally regulated genes. ChIP analyses suggested that CHD4 controls chromatin association with JARID1A and modulates H3K4 levels at the promoter and coding regions of target genes. We further demonstrated that the C. elegans homologues of JARID1 and CHD4 function in the same pathway during vulva development. Taken together, these results suggest that JARID1A and the NuRD complex cooperatively function to control developmentally regulated genes. Genome-wide transcriptomic analysis of HeLa cells transfected with JARID1A complex component siRNA
2014-02-21 | E-GEOD-55206 | biostudies-arrayexpress
Project description:Histone H3K4 methylation has been linked to transcriptional activation. JARID1A (also known as RBP2 or KDM5A), a member of the JARID1 protein family, is an H3K4 demethylase, previously implicated in the regulation of transcription and differentiation. Here we show that JARID1A is physically and functionally associated with two histone deacetylase complexes. Immunoaffinity purification of JARID1A confirmed a previously described association with the SIN3B-containing HDAC complex, and revealed an association with the nucleosome remodeling and deacetylase (NuRD) complex. Sucrose density gradient and sequential immunoprecipitation analyses further confirmed the stable association of JARID1A with these two HDAC complexes. JARID1A depletion led to changes in the expression of hundreds of genes, two-thirds of which were also controlled by CHD4, the NuRD catalytic subunit. Gene ontology analysis confirmed that the genes commonly regulated by both JARID1A and CHD4 were categorized as developmentally regulated genes. ChIP analyses suggested that CHD4 controls chromatin association with JARID1A and modulates H3K4 levels at the promoter and coding regions of target genes. We further demonstrated that the C. elegans homologues of JARID1 and CHD4 function in the same pathway during vulva development. Taken together, these results suggest that JARID1A and the NuRD complex cooperatively function to control developmentally regulated genes.
2014-02-21 | GSE55206 | GEO
Project description:p53 inactivation occurs only rarely in neuroblastoma, although miR-34, a transcriptional target of p53, is often deleted in neuroblastoma, suggesting another way in which p53 signaling might be impaired. In this study we show that miR-34 directly targets and downregulates the Polycomb Repressive Complex 2 (PRC2) and its associated histone demethylase, JARID1A, in a p53-dependent manner, 8 samples were transfected with siRNA control or JMJD2B, MYCN, JARID1A into NB1691 cells.
2014-01-01 | E-GEOD-49854 | biostudies-arrayexpress
Project description:Transcription factors and chromatin modifiers play important roles in programming and reprogramming of cellular states during development. Much is known about the role of these regulators in gene activation, but relatively little is known about the critical process of enhancer silencing during differentiation. Here we show that the H3K4/K9 histone demethylase LSD1 plays an essential role in decommissioning enhancers during differentiation of embryonic stem cells (ESCs). LSD1 occupies enhancers of active genes critical for control of ESC state. However, LSD1 is not essential for maintenance of ESC identity. Instead, ESCs lacking LSD1 activity fail to fully differentiate and ESC-specific enhancers fail to undergo the histone demethylation events associated with differentiation. At enhancers, LSD1 is a component of the NuRD complex, which contains additional subunits that are necessary for ESC differentiation. We propose that the LSD1-NuRD complex decommissions enhancers of the pluripotency program upon differentiation, which is essential for complete shutdown of the ESC gene expression program and the transition to new cell states. This represents the expression part of the study.
2012-01-03 | E-GEOD-27714 | biostudies-arrayexpress
Project description:Transcription factors and chromatin modifiers play important roles in programming and reprogramming of cellular states during development. Much is known about the role of these regulators in gene activation, but relatively little is known about the critical process of enhancer silencing during differentiation. Here we show that the H3K4/K9 histone demethylase LSD1 plays an essential role in decommissioning enhancers during differentiation of embryonic stem cells (ESCs). LSD1 occupies enhancers of active genes critical for control of ESC state. However, LSD1 is not essential for maintenance of ESC identity. Instead, ESCs lacking LSD1 activity fail to fully differentiate and ESC-specific enhancers fail to undergo the histone demethylation events associated with differentiation. At enhancers, LSD1 is a component of the NuRD complex, which contains additional subunits that are necessary for ESC differentiation. We propose that the LSD1-NuRD complex decommissions enhancers of the pluripotency program upon differentiation, which is essential for complete shutdown of the ESC gene expression program and the transition to new cell states. This is the ChIP-seq part of the study.
2012-01-03 | E-GEOD-27841 | biostudies-arrayexpress
Project description:RNA polymerase III (Pol III) synthesizes noncoding RNAs essential for translation, RNA processing, and transcription regulation. Its activity aligns with cellular growth and nutrient availability, and its dysregulation is linked to diseases like breast cancer and leukodystrophy. Despite its importance, Pol III regulators remain largely unidentified due to a lack of exploration of Pol III-centered protein-protein interactions (PPIs). To address this need, we conducted high throughput proteomic experiments and identified over 300 novel Pol III interactors, including Pol II-related transcription factors, nuclear import factors, and splicing factors. Most notably, our proteomic survey uncovers complex-complex interactions between Pol III and the NuRD (Nucleosome Remodeling and Deacetylase) complex. NuRD complex is a known Pol II co-repressor, but its recruitment to and effect on Pol III remains uncharacterized. Using innovative large-scale NuRD binding pattern meta-study, NuRD ChIP-seq combined with Pol III inhibition, and Pol III activity profiling in mammalian cell lines, we revealed that the NuRD is recruited by Pol III itself and fine-tunes Pol III transcription activity. We found that NuRD exhibits a binding preference for highly active Pol III genes, and inhibition of Pol III transcription reduced the enrichment of NuRD subunits. Functionally, inhibiting NuRD deacetylase activity releases its inhibition on Pol III transcription and increases its dynamic range. In addition, our ATAC-seq analysis suggests NuRD is potentially involved in establishing nucleosome positioning through its ATP-dependent remodeler activity. Beyond identifying NuRD as a novel Pol III regulator, our survey of Pol III interactions unexpectedly identifies physical interactions between Pol III and mRNA splicing factors. We demonstrate that Pol III depletion leads to rewiring of splicing efficiencies for specific mRNA subpopulations, suggesting a previously unrecognized interplay between Pol III and RNA processing factors. Together, these findings advance our understanding of Pol III interactome, uncovering new layers of transcriptional control and unexpected functional consequences of Pol III interactions in human cells.
2026-07-09 | GSE311392 | GEO
Project description:RNA polymerase III (Pol III) synthesizes noncoding RNAs essential for translation, RNA processing, and transcription regulation. Its activity aligns with cellular growth and nutrient availability, and its dysregulation is linked to diseases like breast cancer and leukodystrophy. Despite its importance, Pol III regulators remain largely unidentified due to a lack of exploration of Pol III-centered protein-protein interactions (PPIs). To address this need, we conducted high throughput proteomic experiments and identified over 300 novel Pol III interactors, including Pol II-related transcription factors, nuclear import factors, and splicing factors. Most notably, our proteomic survey uncovers complex-complex interactions between Pol III and the NuRD (Nucleosome Remodeling and Deacetylase) complex. NuRD complex is a known Pol II co-repressor, but its recruitment to and effect on Pol III remains uncharacterized. Using innovative large-scale NuRD binding pattern meta-study, NuRD ChIP-seq combined with Pol III inhibition, and Pol III activity profiling in mammalian cell lines, we revealed that the NuRD is recruited by Pol III itself and fine-tunes Pol III transcription activity. We found that NuRD exhibits a binding preference for highly active Pol III genes, and inhibition of Pol III transcription reduced the enrichment of NuRD subunits. Functionally, inhibiting NuRD deacetylase activity releases its inhibition on Pol III transcription and increases its dynamic range. In addition, our ATAC-seq analysis suggests NuRD is potentially involved in establishing nucleosome positioning through its ATP-dependent remodeler activity. Beyond identifying NuRD as a novel Pol III regulator, our survey of Pol III interactions unexpectedly identifies physical interactions between Pol III and mRNA splicing factors. We demonstrate that Pol III depletion leads to rewiring of splicing efficiencies for specific mRNA subpopulations, suggesting a previously unrecognized interplay between Pol III and RNA processing factors. Together, these findings advance our understanding of Pol III interactome, uncovering new layers of transcriptional control and unexpected functional consequences of Pol III interactions in human cells.
2026-07-09 | GSE310006 | GEO
Project description:p53 inactivation occurs only rarely in neuroblastoma, although miR-34, a transcriptional target of p53, is often deleted in neuroblastoma, suggesting another way in which p53 signaling might be impaired. In this study we show that miR-34 directly targets and downregulates the Polycomb Repressive Complex 2 (PRC2) and its associated histone demethylase, JARID1A, in a p53-dependent manner,
2014-01-01 | GSE49845 | GEO
Project description:p53 inactivation occurs only rarely in neuroblastoma, although miR-34, a transcriptional target of p53, is often deleted in neuroblastoma, suggesting another way in which p53 signaling might be impaired. In this study we show that miR-34 directly targets and downregulates the Polycomb Repressive Complex 2 (PRC2) and its associated histone demethylase, JARID1A, in a p53-dependent manner,
2014-01-01 | GSE49854 | GEO
Project description:p53 inactivation occurs only rarely in neuroblastoma, although miR-34, a transcriptional target of p53, is often deleted in neuroblastoma, suggesting another way in which p53 signaling might be impaired. In this study we show that miR-34 directly targets and downregulates the Polycomb Repressive Complex 2 (PRC2) and its associated histone demethylase, JARID1A, in a p53-dependent manner, 4 samples were transfected with miRNA control or miR-34a, miR-34b, miR-34c into SK-N-BE2 cells.
2014-01-01 | E-GEOD-49845 | biostudies-arrayexpress