Presentation of an unpaired adenosine in a bulge or internal loop correlates with high-affinity SPEN binding. Minimum free energy secondary structure predictions for XIST A-repeat transcripts. RNA secondary structures are labeled with specific nucleotide sequences (left column) or colored according to the repeat number for XIST A-repeats 1–9 (right column). XIST A-repeat 1 is colored in pink, repeat 2 is orange, repeat 3 is yellow, repeat 4 is olive green, repeat 5 is dark green, repeat 6 is light blue, repeat 7 is dark blue, repeat 8 is violet, and repeat 9 is purple. Gray ovals indicate the location of unpaired adenosines in GUAUC, GAUAC, or GAUAUC sequences within a dsRNA context for each XIST A-repeat region transcript. The specific sequence (or sequences) containing an unpaired adenosine within an internal loop is color-coded by repeat number, and listed to the right of each secondary structure.
