Figure 4

Visualization of incomplete transcripts in the poly(A)- samples. (a) A bimorphic example showing uniform coverage across the complete transcript. Note that the majority of the identified bimorphic transcripts are similar to this. (b) Examples of bimorphic transcripts with non-uniform coverage. Note that both ubr 4 (retinoblastoma-associated factor 600) and nup155 (nucleoporin 155 kDa) show similar normalized read densities in poly(A)+ and poly(A)- samples; however, both exhibit a gradual enrichment toward the 5' ends of the genes (blue dashed lines) in the poly(A)- samples. (c) Examples of non-poly(A)+ transcripts with non-uniform coverage. Note that both sf3b2 (splicing factor 3b, subunit 2) and eif3a (eukaryotic translation initiation factor 3) exhibit a gradual 5' end enrichment (blue dashed lines) in the poly(A)- samples, although both are more abundant in poly(A)+ samples (note the difference in the y-axis). (d) Examples of bimorphic and poly(A)+ transcripts with non-uniform coverage. See text for details.