A multi-cancer CRISPR/Cas9 reveals distinct gene dysregulation by noncoding MSTRG transcripts

Long noncoding RNAs (lncRNAs) regulate gene expression with their functional domains without being translated into proteins. Whether wrong noncoding transcripts have functions is of special interest and lacks systematic investigation. Our study identified several MSTRG transcripts that may have regulatory functions through specific DNA-binding domains (DBDs). We selected three MSTRG noncoding transcripts and validated their roles in cancer through CRISPR/Cas9-mediated knockout experiments, using A549 and HCT116 cell lines as experimental models. Then, we conducted a comparative gene expression analysis using RNA-seq data to compare the knockout of three aberrant human non-coding transcripts to their respective wild-type controls. Overall design: We selected three MSTRG transcripts for knockout of their DNA-binding domains (DBDs), including MSTRG.4401.1, MSTRG.2513.6, and MSTRG.34636.7. Specifically, MSTRG.4401.1 and MSTRG.2513.6 were knocked out in both A549 and HCT116 cell lines, while MSTRG.34636.7 was knocked out only in HCT116 cells. Both before and after the knockout, RNA sequencing (RNA-seq) was performed on the samples.