Similar Datasets
Project description:Previous studies of E2F family members have suggested that protein-protein interactions may be the mechanism by which E2Fs are recruited to specific genomic regions. We have addressed this hypothesis on a genome-wide scale using ChIP-seq analysis of MCF7 cell lines that express tagged wildtype and mutant E2F1 proteins. First, we performed ChIP-seq for tagged wt E2F1. Then, we analyzed E2F1 proteins that lacked the N terminal SP1 and cyclin A binding domains, the C terminal transactivation and pocket protein binding domains, and the internal marked box domain. Surprisingly, we found that the ChIP-seq patterns of the mutant proteins were identical to that of wt E2F1. However, mutation of the DNA binding domain abrogated all E2F1 binding to the genome. These results suggested that the interaction between the E2F1 DNA binding domain and a consensus motif may be the primary determinant of E2F1 recruitment. To address this possibility, we analyzed the in vivo binding sites for the in vitro-derived consensus E2F1 motif (TTTSSCGC) and also performed de novo motif analysis. We found that only 12% of the ChIP-seq peaks contained the TTTSSCGC motif. De novo motif analysis indicated that most of the in vivo sites lacked the 5M-CM-"M-BM-^@M-BM-^Y half of the in vitro derived consensus, having instead the in vivo consensus of CGCGC. In summary, our findings do not provide support for the model that protein-protein interactions are involved in recruiting E2F1 to the genome, but rather suggest that recognition of a motif found at most human promoters is the critical determinant. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf 9 total ChIP-seq datasets; four different HA-ER-E2F1 mutants, and one HA ER E2F1 wild type dataset done in duplicate, from 5 different stable cell lines derived from MCF7 cells; Three Input replicates from 2 different stable cell lines derived from MCF7 cells; HA ER E2F1 wild type duplicate dataset from MCF7 stable cells; 1 HA ER E2F1 DBDmut replicate from MCF7 stable cells cells, 1 HA ER E2F1M-CM-^NM-BM-^TC replicate from MCF7 stable cells cells, 1 HA ER E2F1M-CM-^NM-BM-^TN/C replicate from MCF7 stable cells cells, 1 HA ER E2F1M-CM-^NM-BM-^TMB replicate from MCF7 stable cells cells, 1 HA ER E2F1M-CM-^NM-BM-^TMB replicate from MCF7 stable cells cells, 3 Input replicates from MCF7 stable cells cells.
2011-04-04 | E-GEOD-28286 | biostudies-arrayexpress
Project description:2 biological replicates (array 59066 and array 64695) of HeLa E2F1 ChIP vs matched Total DNA Keywords: ChIP
2006-03-03 | GSE4319 | GEO
Project description:We first trained a set of experimentally identified E2F1 targets by a ChIPModules approach, the identified module of E2F1 and AP-2alpha was validated by ChIP-chip assays. Keywords: ChIP-chip
2006-08-14 | GSE5175 | GEO
Project description:Previous studies of E2F family members have suggested that protein-protein interactions may be the mechanism by which E2Fs are recruited to specific genomic regions. We have addressed this hypothesis on a genome-wide scale using ChIP-seq analysis of MCF7 cell lines that express tagged wildtype and mutant E2F1 proteins. First, we performed ChIP-seq for tagged wt E2F1. Then, we analyzed E2F1 proteins that lacked the N terminal SP1 and cyclin A binding domains, the C terminal transactivation and pocket protein binding domains, and the internal marked box domain. Surprisingly, we found that the ChIP-seq patterns of the mutant proteins were identical to that of wt E2F1. However, mutation of the DNA binding domain abrogated all E2F1 binding to the genome. These results suggested that the interaction between the E2F1 DNA binding domain and a consensus motif may be the primary determinant of E2F1 recruitment. To address this possibility, we analyzed the in vivo binding sites for the in vitro-derived consensus E2F1 motif (TTTSSCGC) and also performed de novo motif analysis. We found that only 12% of the ChIP-seq peaks contained the TTTSSCGC motif. De novo motif analysis indicated that most of the in vivo sites lacked the 5â half of the in vitro derived consensus, having instead the in vivo consensus of CGCGC. In summary, our findings do not provide support for the model that protein-protein interactions are involved in recruiting E2F1 to the genome, but rather suggest that recognition of a motif found at most human promoters is the critical determinant. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
2011-04-04 | GSE28286 | GEO
Project description:MYC binding sites determined in HeLa cells using ChIP-chip Keywords: ChIP-chip
2006-03-09 | GSE4354 | GEO
Project description:E2F transcription factors are known regulators of the cell cycle, proliferation, apoptosis and differentiation. We reveal an essential role for E2F1 in liver through the regulation of glycolysis and lipogenesis. E2F1 deficiency leads to a decreased in glycolysis and de novo synthesis of fatty acids in hepatocytes. ChIP-Seq was performed to determine direct tagets of E2F1 in hepatocytes. We highlight that E2F1 directly binds the promoters of genes implicated in metabolic process and notably key lipogenic genes to control these pathways.
2015-12-01 | GSE74006 | GEO
Project description:E2F1, the first member of E2F family transcription factors, plays a central role in cell cycle progression, DNA-damage response and apoptosis. Accumulating evidence indicates that E2F1 regulates replication of several DNA viruses. We and others previously described deregulated E2F1 expression during Epstein-Barr virus (EBV) induced B-cell transformation and its role in survival of transformed B-lymphocytes in response to DNA-damage signals. In addition, global transcriptomic analyses (GSE235941, GSE237484) reveal that E2F1 expression is transcriptionally activated during EBV latent infection in B-lymphocytes but suppressed during lytic-cycle reactivation. However, the precise regulations by which E2F1 sustains EBV latent to lytic switch remains unanswered. Given that E2F activity is often deregulated by infection with DNA viruses, the main objective of our study was to investigate the genome-wide occupancy of E2F1 on both cellular and viral gene promoters, driving EBV pathogenesis.
2025-06-12 | GSE285456 | GEO
Project description:The SETD6 protein lysine methyltransferase has a role in the regulation of various cellular processes including cancer initiation and progression. It methylates several cellular proteins including K117 of the E2F1 transcription factor, but the functional consequences of this methylation event are unknown. In this study, the role of SETD6 mediated E2F1 methylation on the progression of prostate cancer was investigated. We identified distinct sets of genes that are bound and upregulated by methylated and unmethylated E2F1. Genes upregulated by methylated E2F1 lead to the negative regulation of cell migration, while genes upregulated by unmethylated E2F1 have roles in cell proliferation and apoptosis. BRD4 is known to bind E2F1 acetylated at K117 and K120. Here, we demonstrate that methylation of E2F1 at K117 prevents E2F1-BRD4 binding of in vitro and in cells establishing the molecular mechanism of the differential gene regulation by methylated and unmethylated E2F1 that depends on SETD6 activity.
2025-12-22 | GSE286198 | GEO
Project description:The SETD6 protein lysine methyltransferase has a role in the regulation of various cellular processes including cancer initiation and progression. It methylates several cellular proteins including K117 of the E2F1 transcription factor, but the functional consequences of this methylation event are unknown. In this study, the role of SETD6 mediated E2F1 methylation on the progression of prostate cancer was investigated. We identified distinct sets of genes that are bound and upregulated by methylated and unmethylated E2F1. Genes upregulated by methylated E2F1 lead to the negative regulation of cell migration, while genes upregulated by unmethylated E2F1 have roles in cell proliferation and apoptosis. BRD4 is known to bind E2F1 acetylated at K117 and K120. Here, we demonstrate that methylation of E2F1 at K117 prevents E2F1-BRD4 binding of in vitro and in cells establishing the molecular mechanism of the differential gene regulation by methylated and unmethylated E2F1 that depends on SETD6 activity.
2025-12-22 | GSE286020 | GEO