Hormone response elements for the thyroid receptor-α include specific distal 5'-flanking DNA

Optimal gene transcription is achieved through precise interactions between transcription factors and their DNA binding sites. We provide evidence that conserved distally located 5'-flanking sequences interact directly with the intrinsically disordered amino-terminal region of the thyroid receptor-α (TRα) to control transcriptional activity. Simulated modeling and dynamics with multiple ChIP-seq-derived sequences consistently reveal specific lysine/arginine-DNA minor groove interactions. The impact of these interactions is to distort DNA structural conformations, and these are also revealed with atomic force microscopy. The importance of the 5'-flanking DNA is further emphasized with reporter gene assays and comparisons with canonical response elements. Overall, the study reveals the inadequacy of current definitions of the DNA hormone response element (HRE) and suggests that future descriptions of the HRE include the conserved distal DNA sequences. The broad impact of this study is further underscored by the common occurrence of Lys/Arg-rich motifs within the intrinsically disordered regions of nuclear receptors.