Figure 4.

Integration of RNA-seq and CAGE data. Each panel displays an example of a gene where the usage of alternative transcription start sites explains the patterns of TDU. (A) Coverage tracks (Y-axes) of RNA-seq and CAGE data for cerebral cortex and cerebellum are shown along the genomic coordinates (X-axis) of the locus of gene GAS7, located on chromosome 17. The upper two tracks show RNA-seq data from individual 12ZZX. The lower two tracks show mean CAGE counts (on log₂ scale) for each annotated TSS. Cortex uses two transcription start site clusters (see red arrows) that are absent in cerebellum. The differential usage of these two TSS explains the upstream RNA-seq coverage seen in cortex. (B) Analogous to Figure 4A, showing data of thyroid and subcutaneous adipose tissue along the genomic coordinates of the KRT8 locus on chromosome 12. The RNA-seq data are from individual 11EI6. The internal TSS cluster that is indicated by the red arrow is strongly used in thyroid tissue, resulting in the expression of short transcript isoforms. (C) Same as in Figure 4A, but showing data of heart and pancreas along the genomic coordinates of the NEBL locus on chromosome 10. The RNA-seq data corresponds to the individual ZF29. In heart, the usage of an internal TSS (indicated by the red arrow) results in the expression of transcript isoforms that exclude several 5′ exons of the gene.