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Fig. 6 | Genome Biology

Fig. 6

From: CRISPRi enables isoform-specific loss-of-function screens and identification of gastric cancer-specific isoform dependencies

Fig. 6

Identification of genes that express alternative transcripts with opposing functions. a H3K4me3 signals in the promoter of ZFHX3 in tumour or adjacent normal tissue. Fifty per cent of GC patients show a gain of H3K4me3 at the ZFHX3 promoter. Each bar represents a tumour or normal sample from the indicated GC patient tissue obtained using nano-chip-seq [10]. b Profiles of H3K4me3 signals in two patient samples with a high signal, showing a tumour-specific gain of transcript P2. Bottom panel shows the PacBio reads of ZFHX3 from GC cell lines. c Schematic describing the protein generated from P1 or P2 promoters of ZFHX3. d Violin plot showing the proliferation changes from the CRISPRi screen induced by sgRNAs targeting transcript P2 of ZFHX3. Each dot represents a different sgRNA. e Proliferation changes following CRISPRi-mediated targeting of ZFHX3 transcript P2, measured using crystal violet staining assay in GC cell lines 7 days post-infection. The results are plotted as an average ± SD of two sgRNAs, n = 2. Each dot represents a different sgRNA. f Representative images from e. g Proliferation of YCC3 cells measured 7 DPI with sgRNAs targeting ZFHX3 transcript P2 using BrDU proliferation assay. The results are plotted as an average ± SD, n = 2. Each dot represents an independent experiment. pValue is calculated using t test (p ≤ 0.05). h qPCR of ZFHX3 target genes following the suppression of ZFHX3 transcript P2. RNA extracted 5 DPI with ZFHX3 sgRNAs was used for qPCR of CDKN1A or MYB. The results are plotted as an average ± SD, n = 2. Each dot represents an independent experiment. pValue is calculated using t test (p ≤ 0.05)

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