1. sgRNAs targeting the 5′ coding region of β-catenin are ineffective due to an alternative translation initiation site in exon 3.
sgRNAs targeting the 5′ coding region of β-catenin are ineffective due to an alternative translation initiation site in exon 3. A, scatter plot of CRISPR z-score (x-axis) versus shRNA z-score (y-axis) of 2,722 genes in the colorectal cell line DLD1. β-catenin is one of the few genes that shows a stronger dropout in the shRNA screen compared with the CRISPR screen. B, top, graphical depiction of CTNNB1 genomic locus. The CTNNB1 gene extends over 40kb and contains 16 exons (vertical hatches). Bottom, exon structure of the human CTNNB1 cDNA. Position of the start codon (ATG) as well as an alternative start site (*ATG supported by EMBL transcript ID ENST and UniProtKB-A0A024R2Q3 and P35222). Magnification of exons 2–5 shows the location of each sgRNA relative to the CTNB1 cDNA. The color intensity represents the z-score for each sgRNA. None of the five sgRNAs targeting the 5′ most coding region score by CRISPR (upstream of alternative start codon), whereas 13 of 15 sgRNAs downstream of that site score by CRISPR.
Diana M. Munoz et al. Cancer Discov 2016;6:
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