Figure 7. Analysis of Exon:Intron Ratios and a Comparison of Nascent Transcript Methods.

(A) Reads mapping to approximately 1,450 genes from Cluster 11 (Figure 2) were analyzed for relative exon and intron coverage. The genes were rank-ordered according to splicing levels (length-normalized exon reads over total reads) in the chromatin fraction (blue), and were compared to splicing levels in the nucleoplasm (red) and cytoplasm (green). Similar results were obtained with all gene clusters (data not shown).

(B) RNA-Seq read distributions at Nfkb1 are shown comparing reads from the cytoplasmic (green), nucleoplasmic (red), and chromatin (blue) fractions to data obtained by 4sU-Seq and GRO-Seq (Rabani et al. 2011; Escoubet-Lozach et al. 2011). GRO-Seq was performed with LPS-stimulated bone marrow-derived macrophages. 4sU-Seq was performed with LPS-stimulated bone marrow-derived dendritic cells. The fifth track displays the 4sU-Seq data with a scale of 15 reads to show the reduced number of reads after the polyadenylation site relative to the last intron. The cleavage site (red arrow) and reads representing transcription past this site (green bracket; abundant only in the GRO-Seq data set) are indicated. See also Figure S7.