Fig. 1

CRISPRi as a tool for inhibition of specific promoter-driven transcript isoforms. a Structure of the HNF4A gene. Isoforms P1 and P2 are marked. CAGE-Seq peaks from the FANTOM project [19] are shown in the bottom panel. b qRT-PCR quantification of HNF4A transcript P1 following CRISPRi-mediated suppression of transcript P1 or P2. Data is shown as mean ± SD, n = 2. pValue is calculated using two-tailed unpaired t test (***p ≤ 0.001). c qRT-PCR quantification of HNF4A transcript P2 following CRISPRi-mediated suppression of transcript P1 or P2. Data is shown as mean ± SD, n = 2. pValue is calculated using two-tailed unpaired t test (***p ≤ 0.001). d Structure of the IMP3 gene. Isoforms P1 and P2 are marked. CAGE-Seq peaks from the FANTOM project are shown in the bottom panel. e Violin plot showing IMP3 dependency following CRISPRi-mediated suppression of different isoforms in GC cell lines. Dots represent individual sgRNAs targeting the indicated IMP3 transcript isoform. pValue is calculated using two-tailed unpaired t test (****p ≤ 0.0001, *p ≤ 0.05). f Distribution of sgRNAs targeting different transcript isoforms of 55 pan cell-essential transcripts. Green, negative control sgRNAs. Purple, sgRNAs targeting the highest expressed (based on RNA-Seq) transcript isoform. Red, sgRNAs targeting the low expressed (based on RNA-Seq) transcript isoform