Homo sapiens Raw sequence reads. Homo sapiens

CRISPR/CAS9 (epi)genome editing brought revolutionary changes to the field of gene and celltherapy. However, a major concern is the potential off-target effects. A comprehensive analysisof the host transcriptome including mRNA, lncRNA, and alternative splicing was done usinghuman cell line expressing the dead Cas9-mediated synergistic activation mediator (dCas9-SAM) plus HIV long terminal repeat (LTR)-specific MS2-mediated single guide RNA (msgRNA).The control scrambled msgRNA (LTR-Zero), and two LTR-specific msgRNAs (LTR_L andLTR_O) groups show very similar expression profiles of the whole transcriptome. Among 839identified lncRNAs, none exhibited significantly different expression in LTR_L vs. LTR-Zerogroup. In LTR_O group, only TERC and scaRNA2 lncRNAs were significantly decreased.Among 142,791 mRNAs, four genes were differentially expressed in LTR_L vs. LTR-Zerogroup. There were 21 genes significantly downregulated in LTR_O vs. either LTR-Zero orLTR_L group and one third of them are histone related. The distributions of different types ofalternative splicing were very similar either within or between groups. There were no apparentchanges in all the lncRNA and mRNA transcripts between LTR_L and LTR-Zero groups. This isthe most comprehensive study of its kind to date demonstrating the rare off-target effects of theHIV-specific dCas9-SAM system in human cells.