RNA-seq analysis after transcription factors overexpression in GI-MEN cells [Part 2]
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE214795 | GEO | 2023/11/21
REPOSITORIES: GEO
Similar Datasets
Project description:RNA-seq analysis was performed in a Neuroblastoma cell line (GI-MEN) to analyze gene expression changes after ASCL1 overexpression.
2023-11-21 | GSE214794 | GEO
Project description:Cut & Run analysis was performed in an neuroblastoma cell line to analyze DNA bindings of ASCL1-tag-HA in GI-MEN ASCL1-tag-HA cells and GI-MEN ASCL1-tag-HA+4TFs cells; analyze DNA bindings of MYCN, PHOX2B and H3K27ac in, GI-MEN 4TFs cells, and GI-MEN ASCL1-tag-HA+4TFs cells.
2023-11-21 | GSE214793 | GEO
Project description:ChIP-seq analysis was performed in an neuroblastoma cell line to analyze DNA bindings of H3K27ac in GI-MEN DOX-ASCL1 cells and ASCL1-HA in GI-MEN DOX-ASCL1-tag-HA cells.
2023-11-21 | GSE214791 | GEO
Project description:H3K27ac HiChIP analysis was performed in GI-MEN DOX-ASCL1 cells to analyze active chromatin-chromatin interactions in GI-MEN DOX-ASCL1 cells.
2023-11-21 | GSE214792 | GEO
Project description:ATAC-seq analysis was performed in an neuroblastoma cell line to analyze chromatin opening of Gi-MEN cells under four different conditions.
2023-11-21 | GSE214790 | GEO
Project description:Neuroblastoma is an embryonic malignancy originating from early nerve cells. Neuroblastoma retains plasticity, interconverting between the mesenchymal (MES) and adrenergic (ADRN) states, which are controlled by different sets of transcription factors forming the core regulatory circuit (CRC). However, their functional roles and cooperative mechanisms in neuroblastoma pathogenesis are poorly understood. Here, we demonstrate that overexpression of ASCL1 in MES neuroblastoma cells opens closed chromatin at the promoters of key ADRN genes, accompanied by epigenetic activation and establishment of enhancer-promoter interactions, thereby initiating subtype switching. ASCL1 inhibits the TGFb-SMAD2/3 pathway but activates the BMP-SMAD1-ID3/4 pathway, serving as negative feedback to balance the function of ASCL1-TCF12 dimers. ASCL1 and other ADRN CRC members potentiate each other’s activity, increasing the expression of the original targets and inducing a new set of genes, thereby promoting conversion to ADRN neuroblastoma. Thus, via its pioneer factor function, ASCL1 serves as a master regulator that characterizes ADRN neuroblastoma.
2023-12-08 | PXD037670 | Pride
Project description:Plants monitor and integrate temperature, photoperiod and light quality signals to respond to continuous changes in their environment. The GIGANTEA (GI) protein is central in diverse signaling pathways, including photoperiodic, sugar and light signaling pathways, stress responses and circadian clock regulation. Previously, GI was shown to activate expression of the key floral regulators CONSTANS (CO) and FLOWERING LOCUS T (FT) by facilitating degradation of a family of CYCLING DOF FACTOR (CDF) transcriptional repressors. However, whether CDFs are implicated in other processes regulated by GI remains unclear. We investigated the contribution of the GI-CDF module to traits that depend on GI. Transcriptome profiling indicated that mutations in GI and the CDFs have antagonistic effects on expression of a wider set of genes than CO and FT, whilst other genes are regulated by GI independently of the CDFs. Detailed expression studies followed by phenotypic assays showed that the CDFs function downstream of GI to control responses to freezing temperatures and growth, but are not necessary for proper clock function. Thus GI-mediated regulation of CDFs contributes to several processes in addition to flowering, but is not implicated in all of the phenotypes influenced by GI. Seedlings of Col-0, the cdf1-R cdf2-1 cdf3-1 cdf5-1 quadruple mutant, gi-100 and gi-100 cdf1-R cdf2-1 cdf3-1 cdf5-1 quintuple mutant were grown for 10 days under LD conditions (16h light/8h dark). The aerial part of the seedlings was collected at ZT12 and RNA was prepared from three biological replicas
2015-07-31 | E-GEOD-59996 | biostudies-arrayexpress
Project description:Plants monitor and integrate temperature, photoperiod and light quality signals to respond to continuous changes in their environment. The GIGANTEA (GI) protein is central in diverse signaling pathways, including photoperiodic, sugar and light signaling pathways, stress responses and circadian clock regulation. Previously, GI was shown to activate expression of the key floral regulators CONSTANS (CO) and FLOWERING LOCUS T (FT) by facilitating degradation of a family of CYCLING DOF FACTOR (CDF) transcriptional repressors. However, whether CDFs are implicated in other processes regulated by GI remains unclear. We investigated the contribution of the GI-CDF module to traits that depend on GI. Transcriptome profiling indicated that mutations in GI and the CDFs have antagonistic effects on expression of a wider set of genes than CO and FT, whilst other genes are regulated by GI independently of the CDFs. Detailed expression studies followed by phenotypic assays showed that the CDFs function downstream of GI to control responses to freezing temperatures and growth, but are not necessary for proper clock function. Thus GI-mediated regulation of CDFs contributes to several processes in addition to flowering, but is not implicated in all of the phenotypes influenced by GI.
2015-07-31 | GSE59996 | GEO
Project description:GIGANTEA (GI) is an important modulator of plant circadian system. Recent studies have reported that protein GI is localized in both nucleus and cytosol, and nuclear and cytosolic GI exert differential effect on plant circadian clock. We first generated GI-null mutants and transgenic Arabidopsis plants that expressed GI fused to green fluorescent protein gene (GIpro::GI-GFP) and GI-GFP with a nuclear localization signal (GIpro::GI-GFP-NLS) or with a nuclear export signal (GIpro::GI-GFP-NES) under the control of native promoter in GI-null mutants. To investigate differential roles of nuclear and cytosolic GI in regulating plant circadian clock, we performed genome-wide gene expression profiling for wild-type plants and the GI-transgenic plants at morning and evening, and analyzed complementation patterns of gi-2 lesion by nuclear and cytosolic GI. As a result, we identified four complementation patterns representing genes affected by only nuclear GI (GIN) or cytosolic GI (GIC), those by either GIN or GIC, and those by the action of both GIN and GIC. Furthermore, we compared the transgenic plants expressing GIpro::GI-GFP with WT and the other GI-transgenic plants to confirm whether abnormally expressed genes by the gi-2 mutation can be complemented by restoring protein GI. Wild-type plants (Col), GI-null mutants (gi-2), and the other transgenic gi-2 plants expressing GIpro::GI-GFP (called GI plants), GIpro::GI-GFP-NLS (called GI-NLS plants), and GIpro::GI-GFP-NES (called GI-NES plants) were grown for seven days under conditions of 16 h light and 8 h dark (LD) and harvested at 1h (ZT1) and 16 hr (ZT16) after the light is turned on, representing morning and evening, respectively. mRNA levels were measured from three biological replicates of Col, gi-2, GI-NLS, GI-NES, and GI.
2013-09-01 | E-GEOD-47169 | biostudies-arrayexpress
Project description:GIGANTEA (GI) is an important modulator of plant circadian system. Recent studies have reported that protein GI is localized in both nucleus and cytosol, and nuclear and cytosolic GI exert differential effect on plant circadian clock. We first generated GI-null mutants and transgenic Arabidopsis plants that expressed GI fused to green fluorescent protein gene (GIpro::GI-GFP) and GI-GFP with a nuclear localization signal (GIpro::GI-GFP-NLS) or with a nuclear export signal (GIpro::GI-GFP-NES) under the control of native promoter in GI-null mutants. To investigate differential roles of nuclear and cytosolic GI in regulating plant circadian clock, we performed genome-wide gene expression profiling for wild-type plants and the GI-transgenic plants at morning and evening, and analyzed complementation patterns of gi-2 lesion by nuclear and cytosolic GI. As a result, we identified four complementation patterns representing genes affected by only nuclear GI (GIN) or cytosolic GI (GIC), those by either GIN or GIC, and those by the action of both GIN and GIC. Furthermore, we compared the transgenic plants expressing GIpro::GI-GFP with WT and the other GI-transgenic plants to confirm whether abnormally expressed genes by the gi-2 mutation can be complemented by restoring protein GI.
2013-09-01 | GSE47169 | GEO