Gene expression profiling of HUDEP-2 cells edited with either ZNF410 targeting or control sgRNA

RNA sequencing was performed of HUDEP-2 cells edited at either ZNF410 or AAVS1 (control locus) to measure gene expression changes due to loss of ZNF410 expression. CHD4 was the most significantly downregulated gene upon ZNF410 editing. We observed that ZNF410 binds to DNA upstream of the CHD4 gene. To test the requirement of ZNF410 binding for CHD4 expression we generated a HUDEP-2 clone in which this region of ZNF410 binding was deleted (CHD4 6.7 kb element deletion clone). We performed RNA-seq of CHD4 6.7 kb element deleted HUDEP-2 cells after either ZNF410 or AAVS1 (control locus) editing and only observed 2 differentially expressed genes after ZNF410 editing in CHD4 6.7 kb element deletion cells, consistent with our results that nearly all gene expression changes found after ZNF410 editing are due to changes in CHD4 expression. Four conditions are included in the study - HUDEP-2 cells edited with ZNF410 targeting sgRNA, HUDEP-2 cells edited with AAVS1 control sgRNA, CHD4_delta-6.7kb HUDEP-2 cells (clone C3-19) edited with ZNF410 targeting sgRNA and CHD4_delta-6.7kb HUDEP-2 cells (clone C3-19) edited with AAVS1 control sgRNA. 3 replicates were performed and analysed for each condition.