Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Defining the Myb Transcriptional Program Controlled by via Genome-wide Chromatin Occupancy and Expression Analyses

ABSTRACT: We used the ERMYB cell line (Hogg et al., Oncogene 15, p2885-2898, 1997) as our model system to identify genes regulated by Myb using whole genome microarray expression profiling. ERMYB is a myeloid progenitor cell line derived by transformation of primary cells by an activated form of Myb (CT3-Myb) fused to the ligand binding domain of ERα. In these cells, activation of the ER-Myb fusion protein by estrogen is required to maintain a proliferative progenitor-like phenotype. The cells undergo monocytic differentiation when Myb is inactivated by withdrawal of β-estradiol (β-E2). However, re-induction of Myb within 24 hours can almost fully reverse the differentiation process. This feature enabled us to employ a novel kinetic expression profiling strategy, in that we withdrew β-E2 to inactivate Myb for 24 h, then re-added it for another 6 h and monitored the gene expression across this time course. We reasoned that this strategy may be more likely to identify true Myb target genes than conventional approaches in which differential expression is examined only at the endpoint of induction. To exclude genes that might be responsive to ERα and not Myb we used the parent CT3-Myb cell line and measured the expression changes 6hrs after β-E2 withdraw and excluded those few gene that were differentially expressed. Triplicate total RNA samples from ERMYB cells were collected at 0, 6, and 24 hr after β-E2 withdrawal and 6 hr after β-E2 re-addition. Samples were analyzed by Illumina Mouse Whole Genome arrays (WG6). Probe intensities were variance stabilised and normalized by the Lumi package (Du et al., 2008). Differentially expressed genes were identified by the LIMMA package (Smyth, 2004) and then grouped into different classes according to their kinetic profiles.

ORGANISM(S): Mus musculus

SUBMITTER: paul LEO

PROVIDER: E-GEOD-22486 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Integrated genome-wide chromatin occupancy and expression analyses identify key myeloid pro-differentiation transcription factors repressed by Myb.

Zhao Liang L Glazov Evgeny A EA Pattabiraman Diwakar R DR Al-Owaidi Faisal F Zhang Ping P Zhang Ping P Brown Matthew A MA Leo Paul J PJ Gonda Thomas J TJ

Nucleic acids research 20110211 11

To gain insight into the mechanisms by which the Myb transcription factor controls normal hematopoiesis and particularly, how it contributes to leukemogenesis, we mapped the genome-wide occupancy of Myb by chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-Seq) in ERMYB myeloid progenitor cells. By integrating the genome occupancy data with whole genome expression profiling data, we identified a Myb-regulated transcriptional program. Gene signatures for leukemia stem c ...[more]

PMID: 21317192

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Project description:Background: Estrogen receptor (ERα) and aryl hydrocarbon receptor (AHR) are two nuclear receptors involved in regulating gene expression. ERα and AHR are regulated by estradiol(E2) and TCDD respectively. They are also regulated by dietary ligands including 3,3´diindolylmethane (DIM) and resveratrol (RES). DIM is an ERα and AHR agonist, while RES is an ERα agonist and AHR antagonist. Few studies have investigated the impact of RES and DIM on ERα and AHR signaling at a genome-wide level. This study assessed ERα and AHR binding and associated gene expression changes after treatment of MCF-7 human breast cancer cells with DIM, RES, E2, TCDD, and E2+TCDD for 1 hour and 6 hours before ChIP and RNA sequencing respectively. Results: 88% and 86% of the ERα bound sites after RES and DIM overlapped with E2 ERα sites. RES and DIM resulted in 577 and 446 differentially expressed genes (DEGs) respectively compared to 866 after E2. 68% and 62.3% of the DEGs after RES and DIM were closest to an ERα binding site. Motif analysis indicated enrichment for AHRE motif among DIM ERα sites but not among E2 or RES ERα sites. Both DIM and E2+TCDD resulted in greater genome wide binding of AHR than TCDD. DIM and E2+TCDD resulted in 10546 and 8904 AHR and ERα co-occupied sites respectively. While co-occupied sites for both enriched for the AHR and ERE motif among others, DIM mediated co-occupied sites enriched for Tcfcp2l1, Tgif1, Gata3 motifs while E2+TCDD mediated ones enriched for the NF1 and Ppara motifs. Overlap of coregulated DEGs after DIM and E2+TCDD indicated 123 were the same among both with 81 and 85 unique coregulated DEGs respectively. Enrichment analysis indicated that more enrichment terms were different than similar for coregulated genes after E2+TCDD and DIM. Conclusions: AHR activation is responsible for DIM mediated reduced regulation of gene expression by ERα relative to E2 and only a subset of the DEG’s after DIM and RES are ERα targets indicating future studies into other transcription factors regulated by DIM and RES are needed for insights into the regulation of gene expression by these ligands.

Dataset Information

Defining the Myb Transcriptional Program Controlled by via Genome-wide Chromatin Occupancy and Expression Analyses

Publications

Integrated genome-wide chromatin occupancy and expression analyses identify key myeloid pro-differentiation transcription factors repressed by Myb.

Similar Datasets

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