Generation of mouse ES cell lines engineered for the forced induction of transcription factors

Abstract

Here we report the generation and characterization of 84 mouse ES cell lines with doxycycline-controllable transcription factors (TFs) which, together with the previous 53 lines, cover 7-10% of all TFs encoded in the mouse genome. Global gene expression profiles of all 137 lines after the induction of TFs for 48 hrs can associate each TF with the direction of ES cell differentiation, regulatory pathways, and mouse phenotypes. These cell lines and microarray data provide building blocks for a variety of future biomedical research applications as a community resource.

Figure 1. Induction of transcription factors (TFs) in ES cells:

(a) plasmid structure that includes loxP recombination sites, puromycin resistance gene, open reading frame (ORF) of a TF with hCMV promoter followed by His6-FLAG tag; (b) schematic diagram showing the expression of transgenic TF induced in Dox- conditions; (c) examples of scatterplots of gene expression in Dox- versus Dox+ condition. Green and red dots indicate genes that are differentially expressed with statistical significance (FDR<0.05, change >1.5 fold); (d) Increase of transcription factor expression after the induction of a transgene, as measured by qPCR (Dox- vs. Dox+); results from two biological replicates (3 technical replicates each); error bars (S.E.M.; ANOVA); and dashed line = 2 fold change; (e) a list of TFs and the number of genes up- or down-regulated by the induction of the TF (FDR<0.05, change >1.5 fold) (Supplementary Table S2).

Figure 2. Correlation of gene expression response to the induction of TFs with tissue-specific gene expression from the GNF ver. 3 database.

Figure 3. Enrichment of gene sets associated with mouse phenotypes from GAD database among genes that were upregulated (positive) or downregulated (negative) after the induction of various TFs.

Figure 4. Enrichment of gene sets associated with various functions and signaling pathways from msigdb ver. 3 database among genes that were upregulated (positive) or downregulated (negative) after the induction of various TFs.