Extended Data Fig. 8: DoubleDAP-seq analysis.
From: Transcription factor binding divergence drives transcriptional and phenotypic variation in maize
a, Schematic showing the doubleDAP-seq assay in which putative heterodimeric TF-DNA complexes can be pulled down and compared to results from a single protein DAP-seq assay to assess binding site specificity differences. b, Neighbor-joining phylogeny based on amino acid similarity of group VII (blue) and group VIII (green) bHLHs from maize and Arabidopsis. Members that were tested in DAP-seq are shown in bold. Three members that were tested in DAP-seq that did not yield any peaks are shown in italics. c, AlphaFold prediction of BHLH85 homodimer. d, Normalized RNA-seq expression (TPM; transcripts per million) of group VIII and VII bHLHs showing heterodimer pairs are co-expressed in many tissues. Normalized expression data from Walley et al.98. e, Venn diagram showing low degree of overlap between Q-A-R (subclade VIII) homodimers and Q-A-R:ZmSPT (subclade VII) heterodimers as exemplified by HALO-BHLH113 (Q-A-R bHLH) in single DAP and HALO-BHLH113:SBPTag-BHLH125/ZmSPT1 in doubleDAP. Only 2% of HALO-BHLH113 peaks were captured in the doubleDAP dataset indicating that the heterodimer configuration is preferred relative to the homodimer.
