Expression profiling in Wild-type and C-JUN knockout MEFs treated with IFNgamma and cycloheximide

ABSTRACT: STAT1 is the major transcription factor (TF) driving response to exposure to IFNg. C-JUN is a TF which has been shown to bind with STAT1 and act as a partner TF. We have expression profiled WT and CJUN-/- MEFs in order to determine the set of IFNg genes regulated by STAT1 and C-JUN. This study was designed primarily to test the accuracy of in silico cis-regulatory module prediction algorithm called SCRM. The set of genes differentially expressed after IFNg are likely to be targets of the TF STAT1. A subset of these genes will also be targeted by partner TFs of STAT1 (e.g. C-JUN). By measuring the expression of the WT IFNg responsive genes in a C-JUN-/- model, the subset of genes that are regulated by C-JUN can be ascertained. This set of genes can then be compared against those predicted to be regulated by C-JUN using the in silico approach SCRM, and therefore the accuracy of the in silico predictions can be determined. Cells were treated with both IFNg and cycloheximide (CHX) to determine direct target genes of the TF STAT1. CHX was added to reduce the downstream response of IFNg treatment (via inhibition of protein synthesis) , resulting in a high quality list of genes directly targeted by STAT1. CHX treatment also allowed for a longer (3hr rather than 1hr) IFNg treatment time, resulting in a more robust IFNg gene signature. Microarrays were analysed using the aroma package in R and the differentially expressed genes were determined through analysis using the limma package. Genes were ranked based on the FDR adjusted p-value calculated using a t-test between IFNg + CHX treated cells and untreated cells (in both WT and C-JUN-/- MEFs). Significantly upregulated genes (P<0.05) were considered direct targets of STAT1.

ORGANISM(S): Mus musculus

SUBMITTER: Geoff Macintyre 

PROVIDER: E-GEOD-26205 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress