Xenbase Image ID: 137431

Figure 1. Rapid Genome-wide Transcriptional Reprogramming in the Absence of Protein Synthesis(A) Experimental design for the RNA-seq analysis of newly transcribed mRNAs before and after NT to Xenopus oocytes. BrUTP is used to label newly transcribed RNAs.(B) Venn diagram of genes classified as activated (reprogrammed), continuously transcribed (maintained), or repressed (downregulated) after NT based on log2 count per million (log2 CPM donor cell divided by NT). False discovery rate (FDR) < 0.05. Results are based on three independent experiments.(C) Representative examples of GO terms significantly enriched (FDR < 0.05) in genes upregulated (reprogrammed genes in Figure 1B) and downregulated (downregulated genes in Figure 1B) after nuclear transfer.(D) Highly expressed genes in Xenopus oocytes tend to be highly expressed in transplanted nuclei. Box plots of gene expression data, with boxes demarcating the 25th–75th percentile and the median indicated by black lines. Whiskers extend to the most extreme data points with a distance to the box at most 1.5 times the box height. Expression levels are compared by reads per kilobase per million (RPKM) values. Statistical significance was calculated using t test; p < 10−16.(E) Hierarchical clustering of gene expression from cultured MEFs before NT, mouse orthologs of Xenopus oocytes expressed genes, MEFs after NT to oocytes, mouse ESCs, and two-cell-stage mouse embryos.(F) Differentially expressed genes after NT in the presence or absence of CHX treatment. Genes are considered differentially expressed if log2CPM (control/CHX treatment) shows a FDR value < 0.05. Results are based on three independent experiments.(G) Hierarchical clustering of gene expression from cultured cells before NT, NT oocytes, and NT oocytes with CHX treatment.See also Figure S1 and Tables S1 and S2. Image published in: Jullien J et al. (2014) Image downloaded from an Open Access article in PubMed Central. © 2014 The Authors. The Journal of Physiology published by John Wiley & Sons Ltd on behalf of The Physiological Society Larger Image Printer Friendly View

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