Fig 1: Validation of novel nuclear G4-selective binding proteins.a, Affinity enrichment coupled with western blot analysis of selected candidates for different topologies of G4 structures and control oligonucleotides (G-runs are highlighted in bold). A representative blot from two independent experiments with similar results is shown. b–e, Binding curves (the indicated Kd values were generated by ELISA) for the human recombinant full-length SMARCA4 protein to G4 Kit1, the single-stranded mutant (ss mutKit1) and double-stranded Kit1 (ds Kt1) (b), UHRF1 protein to G4 Kit1, ss mutKit1, Kit1 hemi-methylated dsDNA and ds Kit1 (c), DDX1 protein to G4 Myc, ss mutMyc and ds Myc (d), DDX24 protein to G4 Kit1, ss mutKit1 and ds Kit1 (e) and RBM22 protein to G4 NRAS and its mutant (mutNRAS) (f). Mean and error (± s.d.) are from three independent experiments (n = 3). a.u., arbitrary units.Source data
Fig 2: SMARCA4 is enriched at endogenous G4s.a, Example genome browser view for XYLB, TMCC6 and LARP1. Signal tracks from ChIP-seq and control input as well as consensus peaks are shown for SMARCA4 (black) and G4s (blue). Sequences that have the biophysical potential to form G4s are shown for plus and minus strands (potential G4s, grey). b, Overlap of SMARCA4 and endogenous G4 high-confidence peaks. c, Occupancy profiles of SMARCA4 endogenous G4 sites (left) and potential G4s (right). d, Proportion of SMARCA4 and G4 ChIP-seq peaks across different genomic features. TSS, transcription start site; UTR, untranslated region; TES, transcription end site; Rep, replicate.Source data
Fig 3: Properties of SMARCA4 binding sites.a, Overlap of binding sites identified by SMARCA4 ChIP-seq in K562 chromatin across three biological replicates. Binding sites identified in at least two replicates were considered as high confidence binding sites. b, Binding motifs identified in SMARCA4 binding sites that are marked by or lack and endogenous G4. The top3 motifs identified by EM for Motif Elicitation (MEME)67 analysis are shown.
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