A prominent activation role of CtBP on HOX gene expression along PcG/trxG pathways

Purpose: The goals of this study are to find out CtBP and PcG coregulated targets through transcriptome profiling (RNA-seq). Methods: Kc cell mRNA profiles of 7-day Ctrl and CtBP and ph-p+E(z) RNAi were generated by deep sequencing, in triplicate, using Illumina HiSeqTM 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: hyper-geometric test and the Benjamini Hochberg FDR correction method and TopHat followed by Cufflinks. qRT–PCR validation was performed using SYBR Green assays. Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the drosophila genome (build dm6) and identified 11,282 transcripts in the 9 samples, among which 381 PcG targets were selected for further analysis. Hierarchical clustering of differentially expressed genes divided these targets into three groups named CtBP co-activated genes,CtBP unaffected genes and CtBP co-repressed genes respectivly. RNA-seq data confirmed CtBP co-activated genes contain 22 known homeobox genes, and 4 of these were validated with qRT–PCR. These results suggest that CtBP is selectively required for the activation of PcG-repressed genes, especially the homeobox transcription factors including Hox genes.Conclusions: Our study represents the first detailed analysis of CtBP and PcG coregulated targets. Overall design: Drosophila Kc cell mRNA of 7-day Control and CtBP and ph-p+E(z) RNAi treated samples were generated by deep sequencing, in triplicate, using Illumina HiSeqTM 2000.