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. Overall design: 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).

为完成概念验证并验证长链非编码RNA（long non-coding RNAs，lncRNAs）的靶基因预测结果，我们在3株癌细胞系中开展了3组基因组编辑实验，靶向敲除包含人特异性lncRNAs预测DNA结合结构域（DNA binding domains，简称DBD）的短序列片段。具体操作如下：在HeLa细胞系中敲除包含RP13-516M14.1 DNA结合结构域的157 bp序列，在RKO细胞系中敲除包含RP11-426L16.8 DNA结合结构域的202 bp序列，在SK-MES-1细胞系中敲除包含SNORA59B DNA结合结构域的198 bp序列；上述所有敲除操作均显著改变了对应靶基因的表达水平。
整体实验设计：针对3种人特异性lncRNAs（RP13-516M14.1、RP11-426L16.8及SNORA59B）的敲除样本及其野生型对照样本的RNA测序（RNA-seq）数据，开展比较基因表达谱分析。