Fig. 2

Properties of transcription start sites (TSSs) and promoters. a Different library types show different properties of 5′ UTRs and TSSs for the gene encoding GAPDH (Pf3D7_1462800). DAFT-seq coverage (i) can be used to determine the longest possible 5′ UTR. Long read sequencing with PacBio (ii, iii) can be used to directly link a specific TSS with the rest of the transcript structure. Direct detection of TSSs with 5UTR-seq data (iv) reveals a range of different TSSs, which have different prevalences at different time points (v- vii). The first track (i) illustrates 7 DAFT-seq libraries, showing continuous coverage along the length of the gene, and variable steady state levels of mRNA throughout the time course. The next two tracks show PacBio coverage (ii) and reads (iii); these long reads can link variation in the TSS to the structure of the rest of the transcript. The fourth track (iv) shows the extreme 5′ end of mRNAs detected with all of the 5UTR-seq data. This data can be separated by time point (track v), with examination of individual time points showing that the most common TSS early in the time course (track vi) is further upstream from the coding sequence than the most common TSSs later in the time course (track vii). b Genomic locations of the TSS peaks identified using 5UTR-seq data. The vast majority of the TSS peaks in this data set (90%) fell outside of annotated exons and introns. A small proportion (9%) were within exons, while 1% were within introns. c Patterns in the base composition around TSSs were identified using the precise TSS positions inferred from the 5UTR-seq data. Windows are shown for a 20 nt distance (i) and a 100 nt distance (ii). Calculation of the information content of the base composition for a 1000 nt window shows that it peaks around the inferred TSS. d Number of TSS peaks in broad or sharp categories for each of the seven time points in the 3D7 time course