Dissection of protein and RNA regions required for SPEN binding to XIST A-repeat RNA

SPEN binding changes XIST A-repeat accessibility to chemical probing. SHAPE-MaP reactivity scores per nucleotide for (A) XIST_A6–9+ RNA alone or (B) XIST_A6–9+ RNA bound to SPEN_{RRM 1–4}. (C) deltaSHAPE-MaP analysis of XIST RNA only compared to XIST–SPEN complex calculated from the two data sets above. Nucleotide positions colored in green showed decreased flexibility in the RNA–protein complex, while nucleotide positions colored in purple showed increased flexibility in the RNA–protein complex, compared to XIST_A6–9+ RNA alone. (D) deltaSHAPE-MaP changes in nucleotide flexibility after SPEN binding were mapped onto the predicted secondary structure of XIST_A6–9+ RNA alone. Nucleotide positions colored in green showed decreased flexibility in the RNA–protein complex, while nucleotide positions colored in purple showed increased flexibility in the RNA–protein complex, compared to XIST_A6–9+ RNA alone. Unpaired adenosine sequences in the GAUAC sequence of the XIST A-repeat numbers 7 and 8 are indicated with brackets.