Extended Data Fig. 10: STARR-seq for additional AID-tagged cofactors shows no effect on enhancer activity.

a, Growth curves over a course of four days comparing untreated (solid line) and IAA-treated (dashed line) cells, for BRD7- (left), BRD9- (middle) and MLL1-AID (right) cell line. N = 2 independent replicates. Insets show Western blot for the respective cofactor in cells without and with IAA treatment for 3h. Upon IAA treatment none of the cofactors were detectable either in Western blot or in mass spectrometry. b, Examples of four enhancers detected by STARR-seq in the BAC library. For each enhancer the activity in BRD7-, BRD9- and MLL1-AID cell lines in the BAC-STARR-seq screen with and without IAA treatment is shown (normalized STARR-seq signal for merged replicates), alongside with endogenous chromatin accessibility and histone modifications in wild-type HCT116 cells. For comparison, enhancer activity in different COF-AID cell lines from the genome-wide STARR-seq screen is shown. None of the enhancers are affected by the loss of neither BRD7, BRD9 nor MLL1, while they are sensitive to depletion of other COFs (e.g. BRD4, MED14 or CDK9). c, Differential analysis of STARR-seq enhancer activity for 114 enhancers detected in the BAC library in each COF-AID cell line with and without IAA treatment to assess the effect of COF degradation on enhancer activity. Number of significantly up- or down-regulated enhancers is denoted (FDR ≤ 0.05). Depletion of none of the three COFs has an effect on enhancer activity, suggesting that they are not required for enhancer activity in the unperturbed HCT116 cells.