Figure 1. Genome-wide measurement of transcript isoform diversity using TIF-Seq.

a, The TIF-Seq method consists of RNA oligo capping, generation of full-length cDNA, circularization, and paired-end sequencing. b-c, TIF boundaries agree overall with previous determinations of transcript 5′ starts (b) and 3′ ends (c) derived from tiling array annotations⁵. As expected, TIF-Seq of non-capped mRNAs does not produce many 5′ reads at the annotated transcript start sites (b). d, Complex landscape of the yeast transcriptome in glucose, showing strand-specific RNA-Seq²⁶ in comparison to TIF-Seq 5′ start and 3′ end profiles, as well as TIF-Seq coverage in logarithmic scale (dark red/blue upper tracks). Individual TIFs are represented by red or blue lines (Watson(+) or Crick(−) strand, respectively), each line designating one TIF. Nucleosome positions (green track, darkness indicates significance²⁷), expression measured by tiling arrays (blue heatmap; darkness indicates expression level), and genome annotation⁵ are shown in the centre: annotated ORFs (red and blue boxes for Watson and Crick strands, respectively), their UTRs (black lines), SUTs (yellow boxes), and CUTs (purple boxes). Coordinates are indicated in base pairs. SUT, stable unannotated transcript; CUT, cryptic unstable transcript.