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. Author manuscript; available in PMC: 2015 Sep 25.
Published in final edited form as: Cell. 2014 Sep 25;159(1):188–199. doi: 10.1016/j.cell.2014.08.018

Figure 2. RAP-RNA Captures Both Direct and Indirect RNA-RNA Interactions.

Figure 2

(A) Enrichment for individual transcripts or classes of RNAs. RAP-RNA[FA-DSG] experiments include two replicate U1 and Malat1 purifications (rep1 and rep2) and one Hdac2 purification (negative control).

(B) Each point represents the average U1 RAP-RNA[FA-DSG] enrichment across all introns (black) or exons (gray) for one gene. The x-axis represents the expression of the mature transcript (exons) in input nuclear-enriched RNA in reads per kilobase per million (RPKM).

(C) Comparison of U1 RAP-RNA[FA-DSG] enrichment for the exons (gray) and introns (black) of all genes.

(D) RAP-RNA[FA-DSG] sequencing reads mapping to Gpi1 and (E) Ptbp3, two of the most highly enriched transcripts in U1 RAP-RNA[FA-DSG] (>100-fold versus input). Gray rectangles highlight enriched introns with many U1 motifs (purple).

(F) Enrichment of sequencing reads in RAP-RNA[FA] versus input aggregated across 5’ and 3’ splice sites for all introns (n > 180,000) or (G) U12 introns (n = 588). U1 RAP-RNA[FA] (red) more strongly enriches splice sites than U1 RAP-RNA[FA-DSG] (gray). Each read-pair contributes a count at the position corresponding to the 3’ end of the original RNA fragment for the 5’-splice-site panel and the 5’ end for the 3’-splice-site panel. See also Figure S2.