Knockout of the DNA binding domains in human-specific lncRNAs causes changed expression of target genes

To demonstrate proof of concept and validate the prediction of lncRNAs’ target genes, we performed three cases of genome editing to knock out the short sequences that contain the predicted DNA binding domains (DBD) of human-specific lncRNAs in three cancer cell lines. The knockout of a 157 bp sequence (containing the DBD of RP13-516M14.1) in the HeLa cell line, a 202 bp sequence (containing the DBD of RP11-426L16.8) in the RKO cell line, and a 198 bp sequence (containing the DBD of SNORA59B) in the SK-MES-1 cell line, all caused the significantly changed expression of target genes. Comparative gene expression profiling analysis of RNA-seq data for the knockout of three human-specific lncRNAs (RP13-516M14.1, RP11-426L16.8 and SNORA59B),and their controls (wild types).