Supplementary Figure 2: PRC2 binds nascent RNA at predicted G4-forming sequences at the 5′ end of the first intron.
From: G-tract RNA removes Polycomb repressive complex 2 from genes
(a) Alternative splicing events caused by Suz12 deletion in mouse ESC (blue) and for comparison alternative splicing events occurring during differentiation of ESC to neural progenitor cells. Alternative splicing events were identified with MISO and divided into 5 different types: skipped exons (SE), mutually exclusive exons (MXE), retained introns (RI), alternative 5′ splice sites (A5SS) and alternative 3′ splice sites (A3SS). (b) As Fig. 1c, but displaying the RNA crosslink-density at splice-sites across the genes that either contain (red) or do not contain (blue) a predicted G4 forming sequence -30 to +300 nt around the first 5′ splice site. (c) As Fig. 1c, except that the crosslink density for non-G4 junctions has been normalised by the non-G4 G-nucleotide frequency vs G4 G-nucleotide frequency ratio at each position (PRC2 P=2 × 10−16, FUS P=2 × 10−16). (d) Characterisation of predicted G4-forming sequences at first exon/intron junctions (-30 to 300 nt) that are either crosslinked or not crosslinked to PRC2 in cells (iCLIP FDR < 0.05) in terms of the number of G-tracts, G nucleotides per tract, nucleotides per loop between G-tracts, loop base composition, expression level of the host gene and position of the crosslinked G within G-tracts. This analysis shows that PRC2 does not have a preference for any particular G4 features, except for a lower number of G-tracts per G4 (P=0.02).
