Extended Data Fig. 8: Structural properties of GET causal network.
From: A foundation model of transcription across human cell types
a. Catalogs of TF-TF interactions. Direct interactions include homodimers, intra-family heterodimers, or inter-family heterodimers. Cofactor-mediated interactions may include both cooperative and competitive binding. b. pLDDT plot for the IDR (intrinsically disordered region) and DBD (DNA-binding ___domain) for TFAP2A and ZFX. c. Predicted monomer structure of ZFX. d. Predicted multimer structure of TFAP2A structured domains and ZFX IDR. Red and blue color marks negative and positive electrostatic surfaces, respectively. e. Molecular dynamics simulation (100 ns) of TFAP2A-ZFX IDR (red) and ZFX IDR monomer (purple). Collapsed structure in ZFX IDR monomer is highlighted in rectangle. f. Sequence logo of ZFX and TFAP2A transcription factor binding motifs. g. Immunoblot detection of TFAP2A, ZFX, and β-ACTIN from HeLa cell lysates subjected to co-immunoprecipitation using a TFAP2A antibody. β-ACTIN serves as a loading control in the same gel. Abbreviation: Pre, HeLa cell lysate prior to bead incubation; Post, HeLa cell lysate after bead incubation; IP, immunoprecipitated proteins. B, empty lane. Two independent experiments were repeated with similar results. A representative result was shown. Raw gel image is in Supplementary Fig. 1. h-j. Prediction of structural interactions between SNAI1 N-terminal and EP300 TAZ2 ___domain, SNAI1 N-terminal and EP300 TAZ1 ___domain, and RELA C-terminal and EP300 TAZ1 ___domain. Red and blue color marks negative and positive electrostatic surfaces, respectively.
