The effect of depletion of BRD8 or TIP60 on gene expression in colorectal cancer cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE203236 | GEO | 2023/03/31
REPOSITORIES: GEO
Similar Datasets
Project description:Although BRD8 has been considered to act as a coactivator of the NuA4/TIP60-histone acetyltransferase complex, the role of BRD8 in colorectal cancer cells remains to be elucidated. We explored genomic BRD8-binding sites in human colorectal cancer cells.
2023-03-31 | GSE203615 | GEO
Project description:In this study, we characterize the fusion protein produced by the ZMYND11-MBTD1 translocation in acute myeloid leukemia. We express the fusion protein and necessary controls in K562 Cells. The fusion protein assembles ZMYND11 factor with the full acetyltransferase NuA4/TIP60 complex. The fusion protein leads to mislocalization NuA4/TIP60 complex in gene bodies, thereby increasing H4ac in specific gene targets. Finally, chromatin aberration is linked to aberrant gene expression and spliced isoforms.
2022-06-01 | GSE171673 | GEO
Project description:Transcript buffering entails the reciprocal modulation of mRNA synthesis and degradation rates, ensuring a constant RNA concentration amidst changes in cellular conditions. While an increasing body of research supports a global, non-sequence-specific linkage between mRNA synthesis and degradation, the underlying mechanisms remain elusive. To explore this, we investigated alterations in RNA metabolism following the acute depletion of TIP60/KAT5, the transcriptional coactivator and acetyltransferase subunit of the NuA4 complex, in mouse embryonic stem cells. By combining RNA sequencing of nuclear, cytoplasmic, and newly synthesised transcript fractions with biophysical modelling, we show that TIP60 activates transcription of numerous genes, with substantially fewer genes undergoing transcriptional repression. Surprisingly, specific RNA species' transcription changes triggered by TIP60 depletion were counterbalanced by compensatory adjustments in RNA export and/or stability within the nucleus and in RNA stability within the cytoplasm. These discoveries imply that transcript buffering operates on a gene-specific level and suggest that cells continually monitor RNA molecule counts in nuclear and cytoplasmic compartments to maintain cellular homeostasis.
2024-01-30 | GSE253311 | GEO
Project description:Transcript buffering entails the reciprocal modulation of mRNA synthesis and degradation rates, ensuring a constant RNA concentration amidst changes in cellular conditions. While an increasing body of research supports a global, non-sequence-specific linkage between mRNA synthesis and degradation, the underlying mechanisms remain elusive. To explore this, we investigated alterations in RNA metabolism following the acute depletion of TIP60/KAT5, the transcriptional coactivator and acetyltransferase subunit of the NuA4 complex, in mouse embryonic stem cells. By combining RNA sequencing of nuclear, cytoplasmic, and newly synthesised transcript fractions with biophysical modelling, we show that TIP60 activates transcription of numerous genes, with substantially fewer genes undergoing transcriptional repression. Surprisingly, specific RNA species' transcription changes triggered by TIP60 depletion were counterbalanced by compensatory adjustments in RNA export and/or stability within the nucleus and in RNA stability within the cytoplasm. These discoveries imply that transcript buffering operates on a gene-specific level and suggest that cells continually monitor RNA molecule counts in nuclear and cytoplasmic compartments to maintain cellular homeostasis.
2024-01-30 | GSE253310 | GEO
Project description:Transcript buffering entails the reciprocal modulation of mRNA synthesis and degradation rates, ensuring a constant RNA concentration amidst changes in cellular conditions. While an increasing body of research supports a global, non-sequence-specific linkage between mRNA synthesis and degradation, the underlying mechanisms remain elusive. To explore this, we investigated alterations in RNA metabolism following the acute depletion of TIP60/KAT5, the transcriptional coactivator and acetyltransferase subunit of the NuA4 complex, in mouse embryonic stem cells. By combining RNA sequencing of nuclear, cytoplasmic, and newly synthesised transcript fractions with biophysical modelling, we show that TIP60 activates transcription of numerous genes, with substantially fewer genes undergoing transcriptional repression. Surprisingly, specific RNA species' transcription changes triggered by TIP60 depletion were counterbalanced by compensatory adjustments in RNA export and/or stability within the nucleus and in RNA stability within the cytoplasm. These discoveries imply that transcript buffering operates on a gene-specific level and suggest that cells continually monitor RNA molecule counts in nuclear and cytoplasmic compartments to maintain cellular homeostasis.
2024-01-30 | GSE253312 | GEO
Project description:Background Tip60 (KAT5) is the histone acetyltransferase (HAT) of the mammalian Tip60/NuA4 complex. While Tip60 is important for early mouse development and mouse embryonic stem cell (mESC) pluripotency, the function of Tip60 as reflected in a genome-wide context is not yet well understood. Results Gel filtration of nuclear mESCs extracts indicate incorporation of Tip60 into large molecular complexes and exclude the existence of large quantities of âfreeâ Tip60 within the nuclei of ESCs. Thus, monitoring of Tip60 binding to the genome should reflect the behaviour of Tip60-containing complexes. The genome-wide mapping of Tip60 binding in mESCs by chromatin immunoprecipitation (ChIP) coupled with high-throughput sequencing (ChIP-seq) shows that the Tip60 complex is present at promoter regions of predominantly active genes that are bound by RNA polymerase II (Pol II) and contain the H3K4me3 histone mark. The coactivator HAT complexes, Tip60- and Mof (KAT8)-containing (NSL and MSL), show a global overlap at promoters, whereas distinct binding profiles at enhancers suggest different regulatory functions of each essential HAT complex. Interestingly, Tip60 enrichment peaks at about 200 bp downstream of the transcription start sites suggesting a function for the Tip60 complexes in addition to histone acetylation. The comparison of genome-wide binding profiles of Tip60 and c-Myc, a somatic cell reprogramming factor that binds predominantly to active genes in mESCs, demonstrate that Tip60 and c-Myc co-bind at 50â60 % of their binding sites. We also show that the Tip60 complex binds to a subset of bivalent developmental genes and defines a set of mESC-specific enhancer as well as super-enhancer regions. Conclusions Our study suggests that the Tip60 complex functions as a global transcriptional co-activator at most active Pol II promoters, co-regulates the ESC-specific c-Myc network, important for ESC self-renewal and cell metabolism and acts at a subset of active distal regulatory elements, or super enhancers, in mESCs. Genome- wide binding of Tip60 co-activator complexes
2015-11-06 | E-GEOD-69671 | biostudies-arrayexpress
Project description:Mechanisms regulating gene expression in the airway epithelium underlie its response to the environment. A network of transcription factors (TFs) and architectural proteins, modulate chromatin accessibility and recruit activating or repressive signals. Bromodomain-containing proteins function as TFs or by engaging methyltransferase or acetyltransferase activity to induce chromatin modifications. Here we investigate the role of Bromodomain Containing 8 (BRD8) in coordinating lung epithelial function. Sites of BRD8 occupancy genome-wide were mapped in human lung epithelial cell lines (Calu-3 and 16HBE14o-). CCCTC-Binding Factor (CTCF) was identified as a predicted co-factor of BRD8, based upon motif over-representation under BRD8 ChIP-seq peaks. Following siRNA-mediated depletion of BRD8, differentially expressed genes with peaks of BRD8 occupancy within 20 kb were subject to gene ontology process enrichment analysis. BRD8 targets are enriched for genes involved in the innate immune response and depletion of BRD8 increased the secretion of the antimicrobial peptide beta-defensin 1 and multiple chemokines.
2021-01-29 | GSE158686 | GEO
Project description:Mechanisms regulating gene expression in the airway epithelium underlie its response to the environment. A network of transcription factors (TFs) and architectural proteins, modulate chromatin accessibility and recruit activating or repressive signals. Bromodomain-containing proteins function as TFs or by engaging methyltransferase or acetyltransferase activity to induce chromatin modifications. Here we investigate the role of Bromodomain Containing 8 (BRD8) in coordinating lung epithelial function. Sites of BRD8 occupancy genome-wide were mapped in human lung epithelial cell lines (Calu-3 and 16HBE14o-). CCCTC-Binding Factor (CTCF) was identified as a predicted co-factor of BRD8, based upon motif over-representation under BRD8 ChIP-seq peaks. Following siRNA-mediated depletion of BRD8, differentially expressed genes with peaks of BRD8 occupancy within 20 kb were subject to gene ontology process enrichment analysis. BRD8 targets are enriched for genes involved in the innate immune response and depletion of BRD8 increased the secretion of the antimicrobial peptide beta-defensin 1 and multiple chemokines.
2021-01-29 | GSE158678 | GEO
Project description:In this study, we characterized MORF4L1/MRG15 interactome. Using Flag-ChIP-sequencin K562 cells, we first claimed that both MRG15 isoforms (long or short chromodomain) and MORF4L2/MRGX which does not contain any chromodomain, shared mostly the same targets. Then, we described a new factor associated to MRG15, called EP400NL. EP400NL binds to BRD8 also linked to MRGBP and MRG15/X to form a new complex homolog to the yeast TINTIN. Using RNA-sequencing in BRD8 or MRGBP or MRG15/MRGX and KAT5/TIP60-depleted U2OS cells, we observed that human TINTIN plays a role in gene expression regulation independently of NuA4/TIP60 complex.
2021-08-17 | GSE181533 | GEO
Project description:Background Tip60 (KAT5) is the histone acetyltransferase (HAT) of the mammalian Tip60/NuA4 complex. While Tip60 is important for early mouse development and mouse embryonic stem cell (mESC) pluripotency, the function of Tip60 as reflected in a genome-wide context is not yet well understood. Results Gel filtration of nuclear mESCs extracts indicate incorporation of Tip60 into large molecular complexes and exclude the existence of large quantities of “free” Tip60 within the nuclei of ESCs. Thus, monitoring of Tip60 binding to the genome should reflect the behaviour of Tip60-containing complexes. The genome-wide mapping of Tip60 binding in mESCs by chromatin immunoprecipitation (ChIP) coupled with high-throughput sequencing (ChIP-seq) shows that the Tip60 complex is present at promoter regions of predominantly active genes that are bound by RNA polymerase II (Pol II) and contain the H3K4me3 histone mark. The coactivator HAT complexes, Tip60- and Mof (KAT8)-containing (NSL and MSL), show a global overlap at promoters, whereas distinct binding profiles at enhancers suggest different regulatory functions of each essential HAT complex. Interestingly, Tip60 enrichment peaks at about 200 bp downstream of the transcription start sites suggesting a function for the Tip60 complexes in addition to histone acetylation. The comparison of genome-wide binding profiles of Tip60 and c-Myc, a somatic cell reprogramming factor that binds predominantly to active genes in mESCs, demonstrate that Tip60 and c-Myc co-bind at 50–60 % of their binding sites. We also show that the Tip60 complex binds to a subset of bivalent developmental genes and defines a set of mESC-specific enhancer as well as super-enhancer regions. Conclusions Our study suggests that the Tip60 complex functions as a global transcriptional co-activator at most active Pol II promoters, co-regulates the ESC-specific c-Myc network, important for ESC self-renewal and cell metabolism and acts at a subset of active distal regulatory elements, or super enhancers, in mESCs.
2015-11-06 | GSE69671 | GEO