Fig. 2

RNA protein binding profile from one W-repeat of the IR1 region. a Schematic illustration of the EBNA-LP locus (top) with internal W-repeats. The region used for RBPmap [25] is enhanced (bottom, at scale) and shows the W1 and W2 exons compared to the sisRNA (s1 or s2) introns. Regions amplified for PCR (amplicon) in these studies are shown in purple: a1—ebv-sisRNA-1, a2—ebv-sisRNA-2, a3—sisRNA-1 to W2, a4—W1 to W2, and a5—across both exons. b RNA binding proteins resulting from RBPmap are indicated by region (above, not to scale). Blue indicates proteins assayed by RIP in addition to HNRNPL (bold). c Top results from STRING [38] analysis for enrichment in biological process (top) and KEGG pathway; false discovery rate (FDR) is given. d Fold enrichment of ebv-sisRNA-2 after RIP using HNRNPL, HNRNPD, or normal rabbit IgG antibodies and either BJAB-B1 or Raji cells. Data represent the mean of two independent RIPs per cell line (one for BJAB-B1 HNRNPD) and are normalized to control IgG. See Additional file 3 for individual RIP data point values