YeasTSS: an integrative web database of yeast transcription start sites.

Jonathan Mcmillan,Tae-Hyuk Ahn,Zhenguo Lin,Zhaolian Lu,Judith S Rodriguez

doi:10.1093/database/baz048

Jonathan Mcmillan, Tae-Hyuk Ahn + Show 3 more

Open Access

https://doi.org/10.1093/database/baz048

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Journal: Database	Publication Date: Jan 1, 2019
Citations: 36	License type: CC BY 4.0

Affiliation: Saint Louis University

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.

Highlights

Transcription initiation is the first and probably the most important step in gene expression, as it integrates the actions of key factors involved in transcription regulation [1]
The wide range of divergence times is valuable for studies of the evolutionary dynamic of transcription initiation landscape of promoter structures at different time scales
To illustrate how YeasTSS can be used to visualize the complex and dynamic transcription initiation landscape and promoter structure, we demonstrated an example of using YeasTSS JBrowse genome browser to explore the LAS17 (YOR181W) gene in S. cerevisiae gene (Fig. 2)

Summary

Introduction

Transcription initiation is the first and probably the most important step in gene expression, as it integrates the actions of key factors involved in transcription regulation [1]. Many techniques have been applied to generate genomewide TSS maps, such as microarray [6,7,8], serial analysis of gene expression [9], sequencing of full-length cDNA clones [10], RNA sequencing [11, 12], cap analysis gene expression (CAGE) technique [13, 14], transcript isoform sequencing (TIF-seq) [15] and transcription start site sequencing (TSSseq) [16]. CAGE is probably the most popular TSS interrogation technique and has been used to profile the locations and activities of TSSs in human [17], mouse, fruit fly and zebrafish [4, 13, 18] and the budding yeast Saccharomyces cerevisiae [2]

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