YeasTSS: an integrative web database of yeast transcription start sites

Abstract

The transcription initiation landscape of eukaryotic genes is complex and highly dynamic. In eukaryotes, genes can generate multiple transcript variants that differ in 5' boundaries due to usages of alternative transcription start sites (TSSs), and the abundance of transcript isoforms are highly variable. Due to a large number and complexity of the TSSs, it is not feasible to depict details of transcript initiation landscape of all genes using text-format genome annotation files. Therefore, it is necessary to provide data visualization of TSSs to represent quantitative TSS maps and the core promoters (CPs). In addition, the selection and activity of TSSs are influenced by various factors, such as transcription factors, chromatin remodeling and histone modifications. Thus, integration and visualization of functional genomic data related to these features could provide a better understanding of the gene promoter architecture and regulatory mechanism of transcription initiation. Yeast species play important roles for the research and human society, yet no database provides visualization and integration of functional genomic data in yeast. Here, we generated quantitative TSS maps for 12 important yeast species, inferred their CPs and built a public database, YeasTSS (www.yeastss.org). YeasTSS was designed as a central portal for visualization and integration of the TSS maps, CPs and functional genomic data related to transcription initiation in yeast. YeasTSS is expected to benefit the research community and public education for improving genome annotation, studies of promoter structure, regulated control of transcription initiation and inferring gene regulatory network.

Figure 1

The overall design of YeasTSS. (A) Dataset: The dataset used in YeasTSS is illustrated in this central table. Currently, YeasTSS includes 12 yeast species. The evolutionary relationships of these species are demonstrated by the phylogenetic tree on the left side of data table. The clade of 10 budding yeast species is shaded in green, and the clade of 2 fission yeast species is shaded in yellow. The CP and TSS data of each species were generated by this study. NO data are integrated for S. cerevisiae, Sch. pombe and C. albicans. TFBSs are available in S. cerevisiae and Sch. pombe. For S. cerevisiae, several other functional genomic data are also integrated: TATA-box, DS, HMs, Polymerase II binding (PolII) and TBs obtained from 18 different growth conditions. (B) Genome browser: These data are visualized and integrated by dedicated JBrowse genome browser of each species. (C) Search: The `Search’ utility provides search tools in to retrieve TSS and CP information from gene-by-gene analysis or global approaches. (D) Download: The `Download’ utility allows users to download all raw data used in this database through web interface. (E) Help: The `Help’ page provides documentations about of CAGE technique, TSS identification, inferences of CPs and instructions of using genome browsers.

Figure 2

An Example of using YeasTSS Genome Browser to explore transcription initiation landscape. A 1.5 kb region around the CP region of LAS17 on chrXV (674 807–676 348). The available tracks in S. cerevisiae are provided in the left panel of genome browser. Two consensus CPs on the forward strand are present within 1000 bp upstream of LAS17 ORF. The transcription activity of each CP can be visualized by the TSS tracks. Different CP activities can be observed between the YPD and YPGal (galactose 2%) growth conditions in S. cerevisiae. Only a few tracks were selected in this case. These tracks include: (A) Genome annotation from SGD; (B) consensus CPs; (C) TSS map on plus strand under YPD condition; (D) TSS map on plus strand under YPGal (galactose 2%) condition; (E) TSS map on minus strand under YPD condition; (F) TSS map on minus strand under YPGal condition; (G) nucleosome occupancy under YPD condition; (H) Nucleosome occupancy under YPGal condition; (I) TATA box; (J) position weight matrix (PWM) predicted binding sites; (K) histone modification H3K4me1; (L) histone modification H3K4me2.