Identification of potential target genes of KRAB zinc-finger proteins in cancer cells

KRAB zinc-finger proteins (KZFPs) are potent transcriptional suppressors and suspected to be associated with cancer progression. To identify the potential target genes of KZFPs in lung adenocarcinoma cells, we established a panel of A459 cell lines that over-express 30 types of KZFPs (A549/KZFP cells) and performed RNA-sequencing (RNA-Seq) analysis of these cells. Overall design: The lentivirus vector expressing HA-tagged KZFP was transduced into A459 cells. The ectopic expression of KZFP in A549/KZFP cells was verified by Western blotting with an anti-HA antibody. Total RNA was extracted from the A549/KZFP cells by QIAamp RNA Blood Mini Kit (QIAGEN #52304) and treated with RNase-Free DNase Set (QIAGEN #79254). Quality check of the purified RNA, library construction, and sequencing were performed by Novogene (https://en.novogene.com). Pair-ended and 150bp read length sequencing was performed by Illumina Novaseq6000. Single-replicate experiment was performed for respective A549/KZFP cells, and triplicate experiment was performed for the empty vector-transduced A549 cells.