The YeasTSS Atlas (Yeast Transcription Start Site Atlas) is a primary depository of yeast transcription initiation sites (TSS) data generated by Dr. Zhenguo Lin’s lab at Saint Louis University. These data are valuable for precisely determining the 5’boundary and the 5’untranslated region (5’UTR) of protein coding genes, improving genome annotation quality, and predictions of novel genes, core promoter elements, transcription factor binding sites, and other motifs associated with transcription and inferring gene regulatory network.
The TSS data were obtained by Cap analysis gene expression (CAGE) which identifies genome-wide 5’end of transcripts at a single-nucleotide resolution and simultaneously quantifies their transcription level. In brief, CAGE capture the 7-methyl guanosine cap structure at the 5’end of transcripts, and sequence the transcripts using Illumina. By mapping sequenced reads to a reference genome, the exact 5’ boundaries or TSS locations of a transcript can be identified. The number of reads mapped to a TSS also quantifies the amount of transcripts initiated at the TSS.
Currently, YeasTSS Atlas includes TSS data from 10 budding yeast species (Hemiascomycetes) and two fission yeast species (Schizosaccharomycetes). This database also in integrates other functional genomics data related to transcription initiation and regulation, such as transcription factor binding sites (TFBS), RNA Polymerase II density and histone modification for several well-studied model yeast species, such as Saccharomyces cerevisiae, Schizosaccharomyces pombe and Candida albicans. YeasTSS enables the visualization of these functional genomics data via genome browser JBrowse. YeasTSS also provides a set of queries to search and retrieve TSS and core promoter information from gene-by-gene analysis or global approaches.
All the information in YeasTSS is updated regularly to match the latest data from my lab and recent literatures.