Fig. 6. Comparison of NFY/YY1 sites. (A) An alignment of NFY/YY1 binding sites from the Hoxb4 intron and promoter. The sequence of the forward strand is shown above aligned with the consensus for YY1 (Hyde-DeRuyscher et al., 1995). The sequence of the reverse strand is shown below aligned with the consensus for NFY (Mantovani, 1998). In each case, the core nucleotides of the site are shown in bold. Nucleotides that are unfavourable for binding based upon either consensus are represented in lower case. Variant nucleotides within the core sequences that are thought to abolish YY1 or NFY binding are shown in red. (B) The consensus sequence (forward strand) for the Hoxb4 NFY/YY1 motif. Shown below is a representation of the CR1 NFY/YY1 site. Nucleotides over which YY1 makes base-specific contacts in the major grove are highlighted on the upper strand. Similarly, nucleotides over which NFY makes base-specific contacts in the minor and major grooves are shown on the lower strand. Nucleotides that are predicted to enhance (green) or reduce (red) the affinity of either factor for its site are shown on the appropriate strand. Core nucleotides are shown in bold. (C) Predicted NFY sites from the Hoxc8 early enhancer and the Hox8/Hox7-Hox6 four cluster sequence (H8/7-6 FCS). Sites are shown in the reverse orientation with respect to transcription. The acquisition of alternative CCAAT boxes in the mouse and human HoxC cluster is underlined. Bold, lowercase and red nucleotides have equivalent meanings to those in A.