Fig 1: New insights into NR DNA binding from PBM and ChIP-seq analysis. (A) Half site motif for the indicated NRs along with the amino acid sequence of the P box region in the DNA recognition helix of the first zinc finger in the DBD showing the residues relevant to this work. GR, MR, AR and PR: glucocorticoid, mineralocorticoid, androgen and progesterone receptors, respectively). The only NRs that have P boxes that are not depicted are TLX (NR2E1) with an Asp (D) and Lys (K) and PNR (NR2E3) with an Asn (N) and Lys (K) at positions 69 and 76, respectively (HNF4a numbering). (B) RXRa, COUPTF2 and HNF4a homodimers all bind classical DR1-like motifs (AGGTCAxAGGTCA) while HNF4a homodimers also bind an HNF4-specific binding motif (H4-SBM, xxxxCAAAGTCCA) that is not bound by RXRa or COUPTF2 in the PBMs, nor 11 other NRs in ChIP-seq. (C) RXRa has a preference for the 3' half site in a DR1-like motif in RXR:RXR homodimers as well as in RXR:RAR and RXR:PPAR homodimers, suggesting that an exchange between the 5' RXRa monomer and RAR or PPAR monomers could occur without disrupting the binding of the 3' RXRa monomer. COUPTF2 also prefers the 3' half site of the DR1-like motifs, suggesting it could compete with RXRa homo- or heterodimers on these response elements. (D) PXR, FXRa and RevErba ChIP peaks from mouse liver were all found to be enriched for the H4-SBM but only in the presence of HNF4a, suggesting that they may occupy their own binding sites near HNF4a-bound H4-SBM.