ArticleDatabase : the journal of biological databases and curation2019
YeasTSS: an integrative web database of yeast transcription start sites.
Article in Database : the journal of biological databases and curation, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- The shape of fitness functions and the distribution of mutational effect sizes jointly limit adaptation by regulatory mutations.Nature ecology & evolution · 2026Article
- Intron location and sequence modulate gene expression in Yarrowia lipolytica.Nucleic acids research · 2026Article
- Omics-Based Expression Cassette for Heterologous Protein Production inACS synthetic biology · 2026Article
- Comprehensive mapping of the 5' and 3' untranslated regions ofRNA (New York, N.Y.) · 2026Article
- Deep Generative Model-Driven Design of Microbial Synthetic Promoters.Journal of microbiology and biotechnology · 2025Review
- Comprehensive analysis of Saccharomyces cerevisiae intron structures in vivo.Nature structural & molecular biology · 2025Article
- Alternative translation initiation by ribosomal leaky scanning produces multiple isoforms of the Pif1 helicase.Nucleic acids research · 2024Article
- Species-aware DNA language models capture regulatory elements and their evolution.Genome biology · 2024Article
- Article
- CRISPRi-induced transcriptional regulation of IAH1 gene and its influence on volatile compounds profile in Kluyveromyces marxianus DU3.World journal of microbiology & biotechnology · 2024Article
- ChEC-seq2: an improved Chromatin Endogenous Cleavage sequencing method and bioinformatic analysis pipeline for mappingbioRxiv : the preprint server for biology · 2023Article
- Development and applications of a CRISPR activation system for facile genetic overexpression in Candida albicans.G3 (Bethesda, Md.) · 2023Article
- New insights into genome annotation in Podospora anserina through re-exploiting multiple RNA-seq data.BMC genomics · 2022Article
- TSSr: an R package for comprehensive analyses of TSS sequencing data.NAR genomics and bioinformatics · 2021Article
- Efficient multiplexed gene regulation in Saccharomyces cerevisiae using dCas12a.Nucleic acids research · 2021Article
- Flexible analysis of TSS mapping data and detection of TSS shifts with TSRexploreR.NAR genomics and bioinformatics · 2021Article
- The origin and evolution of a distinct mechanism of transcription initiation in yeasts.Genome research · 2021Article
- Genome-scale reconstruction of Gcn4/ATF4 networks driving a growth program.PLoS genetics · 2020Article
- Extensive 5'-surveillance guards against non-canonical NAD-caps of nuclear mRNAs in yeast.Nature communications · 2020Article
- Parallel Concerted Evolution of Ribosomal Protein Genes in Fungi and Its Adaptive Significance.Molecular biology and evolution · 2020Article
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Authors and funding
5 authors.
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No grant is acknowledged in the PubMed record.
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.
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