Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcriptional profiling by array to study the effect of adenoviruses encoding the FLAG epitope or full-length antisense sequence to Atf3 on transcriptional regulation in rat cardiac myocytes

ABSTRACT: Cardiomyocytes, the terminally-differentiated contractile cells of the heart, undergo hypertrophic growth in response to endothelin-1. This is associated with changes in mRNA expression of immediate early genes (IEGs). Atf3 is a member of the ATF/CREB family transcription factors which bind as dimers to the cAMP response element (CRE). Atf3 mRNA is particularly associated with cell stress responses and is implicated in negative feedback regulation of gene expression. We confirmed that endothelin-1 promotes expression of Atf3 mRNA and protein in cardiomyocytes and that it is an IEG. Atf3 expression was transient and maximal at 0.5-1 h. We used adenoviruses for expression of antisense Atf3 RNA in cardiomyocytes to inhibit upregulation of Atf3 protein in response to endothelin-1. The effects on the cardiomyocyte transcriptome in control cells and cells exposed to endothelin-1 were examined using Affymetrix rat exon 1.0 ST arrays with data analysis using GeneSpring GX11.5. We identified transcripts that were upregulated by endothelin-1 for which antisense Atf3 significantly (FDR<0.05) enhanced or inhibited expression, respectively. The basal levels of other transcripts that are upregulated by endothelin-1 were also increased by antisense Atf3, though antisense Atf3 had no further effect on the response to endothelin-1. The data were validated by quantitative PCR of selected IEG mRNAs examining the effects at different times.

ORGANISM(S): Rattus norvegicus

SUBMITTER: Angela Clerk

PROVIDER: E-MEXP-3392 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Feedback regulation by Atf3 in the endothelin-1-responsive transcriptome of cardiomyocytes: Egr1 is a principal Atf3 target.

Giraldo Alejandro A Barrett Oliver P T OP Tindall Marcus J MJ Fuller Stephen J SJ Amirak Emre E Bhattacharya Bonhi S BS Sugden Peter H PH Clerk Angela A

The Biochemical journal 20120601 2

Endothelin-1 promotes cardiomyocyte hypertrophy by inducing changes in gene expression. Immediate early genes including Atf3 (activating transcription factor 3), Egr1 (early growth response 1) and Ptgs2 (prostaglandin-endoperoxide synthase 2) are rapidly and transiently up-regulated by endothelin-1 in cardiomyocytes. Atf3 regulates the expression of downstream genes and is implicated in negative feedback regulation of other immediate early genes. To identify Atf3-regulated genes, we knocked down ...[more]

PMID: 22390138

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Project description:Maintenance of genetic integrity is essential for survival of all organisms. Activating transcription factor 3 (ATF3) is a member of the c-AMP response element binding (CREB)/ATF family of transcription factors, and is highly inducible by various stress conditions including DNA damage. However, downstream targets and molecular basis underlying pleiotropic effects of ATF3 on the cell fate have been largely unknown. To identify ATF3 targets in the human genome, we carried out chromatin immunoprecipitation-microarray (ChiP-on-chip) and knockdown-expression profiling analysis using two models where ATF3 was either transiently induced or constitutively expressed. We show that ATF3 binds to an unexpectedly large number of targets; 5,984 promoters in HCT116 cells treated with an alkylating agene methyl methanesulfonate (MMS) and 1,423 promoters in LNCaP cells constitutively expressing ATF3. Importantly, targets of MMS-induced ATF3 are highly enriched not only for CREB/ATF motifs but also for binding sites of several stress sensors including DDIT3/CHOP, Egr1, and c-Ets which are concomitantly induced by MMS. Stress-induced ATF3 affects broad but select biological processes including cell cycle, cell death, adhesion, biosynthesis, and receptor signaling pathways. In addition, ATF3 binds to as many as 40% of the p53 targets and preferentially enhances MMS-induced activation of proapoptotic genes such as DR4, DR5, and PUMA, consistent with the proapoptotic effect of ATF3. These data shed new light on the co-regulatory function of ATF3 in the stress-induced transcription factor network. The comprehensive list of genomic targets of ATF3 will facilitate further understanding the role of ATF3 in determining life and death of cells under both physiological and tumour-associated stress conditions. Maintenance of genetic integrity is fundamental to survival of all organisms. DNA damage can be caused by various agents in environment and elicits complex responses in the cell. ATF3 is one of the transcription factors activated by various stress conditions including DNA damage, and has been shown to have pleiotropic effects on life and death of cells depending on the context of experimental conditions. It has been largely unknown, however, which genes and pathways are regulated by stress-induced ATF3. Here we attempted to answer this question by chromatin immunoprecipitation-microarray analysis of downstream targets of ATF3. We show that ATF3 binds to an unexpectedly large number of promoters (nearly 6,000) in a human colorectal cancer cell lineHCT116 treated with an alkylating agent methyl methanesulfonate. Interestingly, the ATF3 targets are highly enriched for binding sites of other stress sensors shedding light on a transcriptional co-regulatory network of DNA damage response. We further show that ATF3 regulates expression of genes in select biological processes including cell cycle, cell death, adhesion, metabolism, signal transduction, and the p53 pathway. The comprehensive list of ATF3 targets provides new insight into a highly inter-connected network of stress-induced transcription factors around ATF3. ChIP-chip samples: Comparison of ATF3-IP and whole genome DNA (control) Gene expression samples: HCT116 cells pre-transfected with either control siRNA or ATF3 knockdown siRNA and stimulated by methyl methanesulfonate (MMS) for 0, 6, 12, and 24 hours

Dataset Information

Transcriptional profiling by array to study the effect of adenoviruses encoding the FLAG epitope or full-length antisense sequence to Atf3 on transcriptional regulation in rat cardiac myocytes

Publications

Feedback regulation by Atf3 in the endothelin-1-responsive transcriptome of cardiomyocytes: Egr1 is a principal Atf3 target.

Similar Datasets

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