Fig. 1

Fig. 1

a A systematic pipeline for identification of canonical (YR) and non-canonical (YC) initiators in the zebrafish developmental promoterome. CTSSs are classified into YR and YC initiators based on CAGE transcription start sites (CTSSs). b UCSC browser views with CAGE data from prim 5 stage to illustrate examples of YR-initiation (apoba) and YC-initiation (rps26) promoters along with a gene promoter with intertwined YR-initiations and YC-initiations (sumo2b). YR-initiations and YC-initiations are shown in blue and red colors respectively. Barplot on the right shows the sum of expression levels of YR-initiations and YC-initiations. Highest CTSS represents the dominant transcription start site. The distance between dominant YR and YC in sumo2b is four nucleotides. c Frequency of position of dominant YC-initiation relative to dominant YR-initiation in dual-initiation promoters. d Contribution of YC-initiation with respect to YR-initiation expression levels in prim 5 stage. The 4151 genes with dual-initiation are sorted according to YC expression levels and grouped into 10% bins. Expression levels (top) and proportion of YC-initiation to total (bottom) are shown. Red dash line indicates 50% cutoff. TPM, tags per million.