Project description:Early growth response gene 1 (EGR1) has been implicated in megakaryocyte differentiation induced by PMA (phorbol 12-myristate 13-acetate). The identification of direct EGR1 target genes in global scale is critical for our understanding of how EGR1 contributes to this process. In this study, we provide a global survey on the binding location of EGR1 in the K562 cell treated by PMA using chromatin immunoprecipitation and massively parallel sequencing (ChIP-Seq). K562 is a human erythroleukemia cell line, which is situated in the common progenitor stage of megakaryocytic and erythroid lineages of the hematopoietic stem cell differentiation and its normally following differentiation is blockaded. Upon exposure to PMA stimuli, K562 cell can be induced into megakaryocytic cell, which provides a model for the study of transcriptional control networks. Over 14 000 highly confident in vivo EGR1 binding sites were identified in PMA treated K562 cell. More than 70% of these genomic sites associated with EGR1 binding were located around annotated gene regions. This whole genome study on the EGR1 targets may help a better understanding of the EGR1 regulated genes and the downstream pathway in megakaryocyte differentiation. The in vivo binding locations of EGR1 in K562 cell treated with PMA (phorbol 12-myristate 13-acetate, 10 ng/ml for 2 hours) were identified using chromatin immunoprecipitation combing with massively parallel sequencing (ChIP-Seq) based on AB SOLiD System 2.0.
Project description:Early growth response gene 1 (EGR1) has been implicated in megakaryocyte differentiation induced by PMA (phorbol 12-myristate 13-acetate). The identification of direct EGR1 target genes in global scale is critical for our understanding of how EGR1 contributes to this process. In this study, we provide a global survey on the binding location of EGR1 in the K562 cell treated by PMA using chromatin immunoprecipitation and massively parallel sequencing (ChIP-Seq). K562 is a human erythroleukemia cell line, which is situated in the common progenitor stage of megakaryocytic and erythroid lineages of the hematopoietic stem cell differentiation and its normally following differentiation is blockaded. Upon exposure to PMA stimuli, K562 cell can be induced into megakaryocytic cell, which provides a model for the study of transcriptional control networks. Over 14 000 highly confident in vivo EGR1 binding sites were identified in PMA treated K562 cell. More than 70% of these genomic sites associated with EGR1 binding were located around annotated gene regions. This whole genome study on the EGR1 targets may help a better understanding of the EGR1 regulated genes and the downstream pathway in megakaryocyte differentiation.
Project description:With anti-EGR1 immunoprecipitated chromatin from mouse prefrontal cortices, we generated EGR1 binding maps with 12, 014 high-confidence peaks. Approximately 81% of EGR1 peaks were within genic regions or nearby promoters, and over 45% EGR1 peaks were in the proximal promoter regions within 1 kb from transcription starting sites.
Project description:Egr1 regulates genes involved in cholesterol biosynthesis in liver. ChIP-chip assays were performed on H4IIE liver cells that were either treated or untreated with insulin for one hour. This experiment includes a custom ChIP-chip design incorporating many genes that are dynamically regulated by insulin signaling. The Egr1 antibody used was from Santa Cruz sc-189. Egr1 ChIP samples from untreated and 1h insulin treated cells were hybridized.
Project description:Egr1 regulates genes involved in cholesterol biosynthesis in liver. ChIP-chip assays were performed on H4IIE liver cells that were either treated or untreated with insulin for one hour. This experiment includes a custom ChIP-chip design incorporating many genes that are dynamically regulated by insulin signaling. The Egr1 antibody used was from Santa Cruz sc-189.