SAFB associates predominantly with intronic regions of protein-coding genes in mouse ESCs. (A) αFLAG western blot of GFP and SAFB rescue in DKO ESCs. (B) Scatter plots showing the correlation of RIP-seq replicate data under each SAFB peak for each genotype. (C) RPM-normalized RIP signal under SAFB peaks in (i) WT and DKO ESCs (αSAFB RIP) and (ii) in SAFB and GFP rescue ESCs (αFLAG RIP). (D) Top three motifs derived from analysis of sequence under SAFB peaks. (E) RNA Input and RIP-seq wiggle density tracks at the Malat1 locus. Black rectangles under wiggle tracks denote the location of SAFB peaks. (F) Genic features that overlap SAFB peaks. (G) Intersection of mm10 annotated repeat elements and SAFB peaks. P-values = (1 − [cumulative distribution function]) of the distribution of intersections observed from 1000 shuffles sets of SAFB peaks. (H) Intersection of repeat-masked elements and multimapping reads from SAFB RIPs in WT and DKO ESCs. “Count,” number of elements in each class that passed the threshold for inclusion. “Obs./Exp,” ratio of observed versus expected genomic space occupied by each class of repeat in the list of elements passing filter (Supplemental Table S2). Classes of repeat that were represented by less than 25 elements in our filtered list were not plotted.
