Fig. 4: Probing activity of TF motifs in episomal and endogenous contexts.
From: Context transcription factors establish cooperative environments and mediate enhancer communication
a, Episomal and genome-integrated STARR-seq design. b, Average log2 episomal STARR-seq activity normalized by the ‘no-TFBS’ fragment (y axis) for homotypic motif repeats (5 bp spacer). Dots represent the three sequence contexts, and lines represent fits for each replicate. Colors reflect TFs and motif classes (compare to a and Fig. 1e). Gray dashed line indicates the no-TFBS reference. c, Two measures of endogenous STARR-seq activity for homotypic motif combinations. Left, fraction of expressed BCs per fragment. Replicates and three sequence contexts are combined. The dashed line indicates the no-TFBS reference. Right, average log2-transformed endogenous STARR-seq activity normalized by the no-TFBS activity. d, Enformer-predicted DNA accessibility for GM12878 for homotypic motif combinations. Individual dots represent the three different sequence contexts.
