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Fig. 1 | Genome Biology

Fig. 1

From: Functional CRISPR screen identifies AP1-associated enhancer regulating FOXF1 to modulate oncogene-induced senescence

Fig. 1

Design of a CRISPR screen targeting AP1 enhancers which are activated upon oncogenic stress. a An example of an enhancer whose activity is induced in response to oncogenic stress. Enhancer activity is inferred from the typical bi-directional transcription of eRNAs (BJ + DMSO indicates proliferating cells and BJ + 4-OHT indicates senescent cells); genomic regions that show DNase hypersensitivity (DHS), as determined by ENCODE, are shown by the gray track). Overall, our GRO-seq analysis identified 1821 regulatory elements (REs; enhancers or promoters) whose activity was induced in BJ cells in face of RAS activation. b De novo motif analysis detected highly significant enrichment of the FOS:JUN (AP1) DNA motif in the REs that were induced upon oncogenic stress. Top: the enriched motif detected in our dataset; bottom: the AP1 motif from the JASPAR DB [49]. c An example for occurrence of an AP1 motif within an enhancer that was induced upon oncogenic stress, that is located close enough to an NGG PAM motif, resulting in Cas9-mediated DNA cleavage that occur within the motif (Cas9 cleavage occurs ~ 3 nt before the PAM). Overall, we identified 398 induced REs with AP1 motif that met this requirement (Cas9 cleavage within a margin of 5 nt with respect to the motif). d Statistical summary of the CRISPR-AP1-EnhLib used in our functional screen

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