Transcriptome-wide response to synthetic chromatin protein PcTF

The goal of this study was to identify genes that become upregulated in response to a synthetic transcription factor, PcTF. PcTF contains a conserved H3K27me3-binding chromodomain expressed in-frame with an mCherry fluorescent tag and a VP64 activation domain. Therefore, we expected genes with H3K27me3-associated promoters to become upregulated upon PcTF expression. We observed that hundreds of genes became up or downregulated. Total RNA was extracted from PcTF-transfected U-2 OS, K562, or SK-N-SH cells, or from a stable U-2 OS cell line that carried a dox-inducible transgene that expressed either full-length PcTF or a truncated "delta-TF" peptide that lacked the histone-binding domain.