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. 2024 Jan 16;20(1):e1011802. doi: 10.1371/journal.pcbi.1011802

Fig 3. A model of cis-regulatory activity driven by diverse TFBSs in wild-type mouse retina.

Fig 3

(A) Design of MPRA library of synthetic CREs with additional lineage-specific TFBSs. CREs contained five sites placed adjacent to the Rho basal promoter. Each CRE contained either three CRX sites and two sites for other TFs (3-1-1) or two CRX sites, two sites for another TF, and one site for a third TF (2-2-1). (B) Observed activity (y-axis) of test set sequences compared to the latent phenotype (x-axis) predicted by the pairwise model. (C) Model parameters representing additive and pairwise contributions of TFBSs averaged across positions. (D) Distribution of position-specific interactions with high-affinity CRX binding sites, broken down by partner TF. (E) MPRA activity of CREs with two (left) or three (right) CRX sites, grouped by TF identity. Each CRE contains sites for CRX and two other TFs. Activity is measured relative to the Rho basal promoter and basal activity is indicated by the dashed line.