An siRNA screen identifies CHD4 as a target for epigenetic therapy

AIM: We performed RNA-sequencing experiments seeking genes whose expression changed after siCHD4 treatment. METHOD: We generated cDNA libraries from RNA purified from SW48 treated by siNegative control, siCHD4, siNegative control plus siDNMT1, siCHD4 plus siDNMT1, siCHD4 plus Decitabine and siNegative control plus Decitabine. We sequenced the cDNA libraries generating single end 50 bp reads on the illumina HiSeq 2500 platform. Sequencing reads were aligned to the human genome hg19 using TopHat RESULTS: We were able to map 23600 genes. 284 genes in siCHD4, 289 genes in siDNMT1, 309 genes in DAC, 1090 genes in siCHD4 plus siDNMT1 and 468 genes in siCHD4 plus siDNMT1 were significantly upregulated at least two fold compared to siNegative control. Overall design: We generated cDNA libraries from RNA purified from SW48 treated by siNegative control, siCHD4, siNegative control plus siDNMT1, siCHD4 plus siDNMT1, siCHD4 plus Decitabine and siNegative control plus Decitabine

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