Fig. 2: Identification of NFIA DNA-binding motifs.
From: Structural basis for genome-wide site-specific DNA recognition by Nuclear Factor IA
a NFIA motif identification based on ChIP-Seq data (experiment ID ENCSR226QQM), obtained from ENCODE, and analyzed using the HOMER algorithm to identify enriched DNA motifs in NFIA-bound regions. Sequence logos derived from the ChIP-Seq analysis were compared with the JASPAR database (matrix ID MA0670.1) to validate motif similarity. b DNA sequences containing NFIA recognition motifs, comprising the half-site (DNA-S) and the full-site (DNA-L) motifs, were utilized in both functional and structural analyses. c, d Biolayer interferometry (BLI) binding profiles of NFIA and NFIADBD with DNA-S. Serial 2-fold dilutions of protein were used, and binding kinetics were analyzed using a 1:1 Langmuir binding model with ForteBio Data Analysis software. e, f BLI binding profiles of NFIA and NFIADBD with DNA-L, following the same experimental setup as DNA-S binding.
