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. Author manuscript; available in PMC: 2019 Jan 10.
Published in final edited form as: Cell Rep. 2018 Nov 19;25(9):2431–2446.e7. doi: 10.1016/j.celrep.2018.11.046

Figure 4. RNPS1 and CASC3 Occupy the Same RNAs and Sites but within Different RNA Pools.

Figure 4.

(A) A Venn diagram showing genes with at least two differentially enriched exons, for which all differentially enriched exons are preferentially bound to CASC3-EJC (blue region), RNPS1-EJC (orange region), or genes with at least one exon enriched in CASC3-EJC and one in RNPS1-EJC (overlap region). The probability of observing an overlap of 5 or fewer genes using a binomial distribution approximating each gene to contain two exons is shown.

(B) An MA-plot showing fold-change in RNPS1-EJC versus CASC3-EJC footprint reads (y axis) against expression levels (x axis). Each dot represents a canonical transcript for each known gene in GRChg38 from UCSC “knownCanonical” splice variant table. Transcripts differentially enriched (p-adjusted < 0.05) in RNPS1-EJC (orange) and CASC3-EJC (blue) are indicated.

(C) Boxplots showing distribution of cytoplasmic/nuclear fraction (y axis) for all (gray), CASC3-EJC-enriched (blue), and RNPS1-EJC-enriched (orange) transcripts. The median values are to the right of each boxplot. Top: p values (Wilcoxon rank sum test). Bottom: number of transcripts in each group. Nuclear/ cytoplasmic transcript level data are from Neve et al. (2016).

(D) Genome browser screenshots showing read coverage along the XIST gene in RNA-seq (top) or RIPiT-seq libraries (labeled on right).

(E) Boxplots as in (C) showing transcript lengths (y axis) of the groups indicated on the x axis. Top: p values (Wilcoxon rank sum test). Bottom: number of transcripts in each group.

(F) Boxplots showing distribution of fold-change values (y axis) for RNPS1-EJC versus CASC3-EJC footprint read counts for all (gray), detained intron-containing (DI+; yellow) or detained intron-lacking (DI−; green) transcripts. (+ve values: RNPS1-EJC enriched; −ve values: CASC3-EJC enriched). Top: p values (Wilcoxon rank sum test). Bottom: number of transcripts in each group. DI+/DI− genes were defined based on Boutz et al. (2015).

(G) Genome browser screen-shot as in (E) for the SRSF5 locus. Note increased RNA-seq reads in introns 4 and 5.

See also Figure S4.