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ChIP-chip analysis of human DREAM complex subunits in G0-arrested and S-phase synchronized cells

ABSTRACT: This experiment is a part of global location analysis of the human DREAM complex including subunits: E2F4, RBL2/p130, LIN9 and LIN54. Specifically, the regions in Human Promoter Array 1.0R (GPL5082) bound by: E2F4 in G0-arrested T98G cells E2F4 in S-phase synchronized T98G cells LIN54 in G0-arrested T98G cells LIN54 in S-phase synchronized T98G cells LIN9 in G0-arrested T98G cells LIN9 in S-phase synchronized T98G cells p130 in G0-arrested T98G cells p130 in S-phase synchronized T98G cells were compared with input chromatin. MAT (Model-based Analysis for Tiling Arrays) .bar and .bed output files provided as supplementary files. Keywords: CHiP-chip genomic DNA

ORGANISM(S): Homo sapiens

PROVIDER: GSE7516 | GEO | 2007/04/17

SECONDARY ACCESSION(S): PRJNA99415

REPOSITORIES: GEO

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Transcription profiling of human T98G cells during cell cycle in T98G

Project description:The mammalian Retinoblastoma (RB) family including pRB, p107, and p130 represses E2F target genes through mechanisms that are not fully understood. In D. melanogaster, RB-dependent repression is mediated in part by the multisubunit protein complex Drosophila RBF, E2F, and Myb (dREAM) that contains homologs of the C. elegans synthetic multivulva class B (synMuvB) gene products. Using an integrated approach combining proteomics, genomics, and bioinformatic analyses, we identified a p130 complex termed DP, RB-like, E2F, and MuvB (DREAM) that contains mammalian homologs of synMuvB proteins LIN-9, LIN-37, LIN-52, LIN-54, and LIN-53/RBBP4. DREAM bound to more than 800 human promoters in G0 and was required for repression of E2F target genes. In S phase, MuvB proteins dissociated from p130 and formed a distinct submodule that bound MYB. This work reveals an evolutionarily conserved multisubunit protein complex that contains p130 and E2F4, but not pRB, and mediates the repression of cell cycle-dependent genes in quiescence. Experiment Overall Design: Gene expression during the cell cycle in T98G cells. Cells were serum starved for 72 hours to induce G0 and then restimuated to enter cell cycle by serum addition. BrdU and FACS was done simultaneously to confirm their cell cycle phase.

2008-06-16 | E-GEOD-8537 | biostudies-arrayexpress

Homo sapiens

Project description:ChIP-chip analysis of human DREAM complex subunits in G0-arrested and S-phase synchronized cells

| PRJNA99415 | ENA

Gene expression profilie during cell cycle in T98G cells

Project description:The mammalian Retinoblastoma (RB) family including pRB, p107, and p130 represses E2F target genes through mechanisms that are not fully understood. In D. melanogaster, RB-dependent repression is mediated in part by the multisubunit protein complex Drosophila RBF, E2F, and Myb (dREAM) that contains homologs of the C. elegans synthetic multivulva class B (synMuvB) gene products. Using an integrated approach combining proteomics, genomics, and bioinformatic analyses, we identified a p130 complex termed DP, RB-like, E2F, and MuvB (DREAM) that contains mammalian homologs of synMuvB proteins LIN-9, LIN-37, LIN-52, LIN-54, and LIN-53/RBBP4. DREAM bound to more than 800 human promoters in G0 and was required for repression of E2F target genes. In S phase, MuvB proteins dissociated from p130 and formed a distinct submodule that bound MYB. This work reveals an evolutionarily conserved multisubunit protein complex that contains p130 and E2F4, but not pRB, and mediates the repression of cell cycle-dependent genes in quiescence. Keywords: Gene expression analysis during cell cycle

2007-07-21 | GSE8537 | GEO

The E2F4/p130 repressor complex cooperates with oncogenic Np73 to promote cell survival

Project description:Tumor suppressor p53 and its related proteins, p63 and p73, can be synthesized as multiple isoforms lacking part of the N- or C-terminal regions. Specifically, high expression of the Np73 isoform is notoriously associated with poor prognosis in cancer. Here, we have performed proteomics analysis of Np73 using as a cellular model human papillomavirus type 38-transformed keratinocytes (38HK) that express high levels of this isoform. We find that Np73 associates with the E2F4/p130 repressor complex through a direct interaction with E2F4. Remarkably, this interaction is favored by the N-terminal truncation of p73 characteristic of Np73 isoforms and is independent of the C-terminal splicing status. We show that the Np73-E2F4/p130 complex is recruited to the promoters of specific genes, thereby enforcing inhibition of their expression both in 38HK and in cancer-derived cell lines. Consistently, silencing of E2F4 in 38HK and in cancer cells resulted in induction of senescence. In conclusion, we have identified and characterized a novel transcriptional regulatory complex that exerts pro-proliferative functions in transformed cells

2023-02-28 | PXD022947 | Pride

Transcriptional profiling of MLL5 Knock down vs. control C2C12 myoblasts (S phase enriched)

Project description:Knockdown of MLL5 led to deregulation of S phase. To understand the molecular basis for this phenotype, we performed microarray analysis of S phase synchronized myoblasts. Genes differentially regulated by MLL5 knock down were revealed by microarray analysis using NIA15K mouse chips. Control and knock down cells were synchronized at G0 by suspension culture and reactivated to enter S phase by replating for 24hrs in growth medium.

2010-05-22 | E-GEOD-14931 | biostudies-arrayexpress

The E2F4/p130 repressor complex cooperates with oncogenic ΔNp73α to promote cell survival in human papillomavirus 38 E6/E7-transformed keratinocytes and in cancer cells

Project description:Tumor suppressor p53 and its related proteins, p63 and p73, can be synthesized as multiple isoforms lacking part of the N- or C-terminal regions. Specifically, high expression of the ΔNp73α isoform is notoriously associated with various human malignancies characterized by poor prognosis. This isoform is also accumulated by oncogenic viruses such as Epstein–Barr virus (EBV), as well as genus beta human papillomaviruses (HPV) that appear to be involved in carcinogenesis. To gain additional insight into ΔNp73α mechanisms, we have performed proteomics analyses using human keratinocytes transformed by the E6 and E7 proteins of the beta-HPV type 38 virus as an experimental model (38HK). We find that ΔNp73α associates with the E2F4/p130 repressor complex through a direct interaction with E2F4. This interaction is favored by the N-terminal truncation of p73 characteristic of ΔNp73 isoforms. Moreover, it is independent of the C-terminal splicing status, suggesting that it could represent a general feature of ΔNp73α isoforms (α, β, γ, δ, ε, ζ, θ, η, and η1). We show that the ΔNp73α-E2F4/p130 complex inhibits the expression of specific genes, including genes encoding for negative regulators of proliferation, both in 38HK and in HPV-negative cancer-derived cell lines. Such genes are not inhibited by E2F4/p130 in primary keratinocytes lacking ΔNp73α, indicating that the interaction with ΔNp73α rewires the E2F4 transcriptional program. In conclusion, we have identified and characterized a novel transcriptional regulatory complex with potential implications in oncogenesis.

2021-06-08 | GSE162816 | GEO

Genome-wide MNase-ChIP profile of transfected Strep-LIN9 in WT and LIN37-/- HCT116 cells

Project description:We performed MNase-ChIP seq with deep digestion to identify the MuvB associated nucleosomes in WT and LIN37 -/- HCT116 cells in G1 arrested and cycling cells. Strep-LIN9 as well as a mutant of the protein (Strep-4xLIN9: R174A/R175A/F180A/F181A) which is unable to associate with LIN37 or RbAP48 were transiently transfected in WT and LIN37 -/- HCT116 cells. At 24 hours after transfection, cells were treated with Nutlin-3a to induce G1 arrest; cells were harvested 48 hours following treatment. For several samples, Nutlin-3a treatment was omitted to maintain cycling conditions. Cells were then cross-linked with formaldehyde, lysed and treated with micrococcal nuclease. Chromatin fragments were precipitated with Streptactin-XT magnetic beads after which DNA was purified and libraries were prepared and sequenced using NovaSeq 6000 platform in 150bp paired-end mode. We find that LIN9 precipitates to +1 nucleosomes of target genes in arrested HCT116 and LIN37 -/- cells. The precipitation of this nucleosome is diminished in cycling cells as well as in arrested cells transfected with the Strep-4xLIN9 mutant.

2022-01-10 | GSE189435 | GEO

Cell cycle-dependent resolution of DNA double-strand breaks repair

Project description:Damage to genomic DNA, especially as DNA double strand breaks (DSB), elicits prompt activation of DNA damage response (DDR) which arrest cell-cycle either G1/S or G2/M to avoid entering S and M phase with DNA damage. In mammalian organs cells are in both proliferating and quiescent states. Quiescent cells are already arrested in G0, therefore there may be fundamental difference in DDR between proliferating and quiescent cells. To address these differences we studied recruitment of DSB repair factors and resolution of DNA lesions induced at site-specific DSBs occurring at different cell cycle phases, i.e. in asynchronously proliferating, G0, and G1 arrested cells. Strikingly, DSBs occurring in G0 quiescent cells are irreparable with a sustained activation of p53-pathway. Conversely, reentry of G0-damaged cells into cell cycle progression, show a delayed clearance of recruited DNA repair factors bound at DSBs, indicating an inefficient repair when compared to DSBs induced in asynchronously proliferating or G1 cells. Moreover, we found that initial recognition of DSBs and assembly of DSB factors is largely similar at different cell cycle phases. Our study thereby demonstrates the crucial role of cell cycle phases in repair and resolution of DSBs.

2015-12-30 | GSE71447 | GEO

Transcription profiling of mouse fibroblasts expressing the 57Bl/6 Ah-receptor vs. Ahr-/- fibroblasts synchronized at G0/G1, S-phase, and in exponential growth

Project description:Role of the Ah-receptor in cell cycle regulation. Mouse fibroblasts expressing the Ah-receptor of C57Bl/6 mice under the regulation of the Tet*Off system were compared to Ahr-/- fibroblasts synchronized at G0/G1, S-phase, or in exponential growth.

2007-08-05 | E-MEXP-996 | biostudies-arrayexpress

Identification of cell cycle-related genes up-regulated during the G2-phase in Giardia lamblia

Project description:To identify the component(s) involved in cell cycle control in the protozoan Giardia lamblia, cells arrested at the G1- or G2-phase by treatment with nocodazole and aphidicolin were prepared from the synchronized cell cultures. RNA-sequencing analysis of the two stages of Giardia cell cycle identified several cell cycle genes that were up-regulated at the G2-phase. This result indicates that the cell cycle machinery operates in this protozoan, one of the earliest diverging eukaryotic lineages.

2019-02-20 | GSE126731 | GEO

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