YeasTSS: an integrative web database of yeast transcription start sites

McMillan, Jonathan; Lü, Zheng; Rodríguez, Juan Luis Rodríguez; Ahn, Tae-Hyuk; Zhang, Lin

doi:10.1093/database/baz048

Cited by 39 publications

(31 citation statements)

References 68 publications

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“…7b). When for those 25 genes all TSSs listed in the yeast TSS database 21 (top 5 abundant TSSs per gene) were analyzed, only a YA motif 22 was identified ( Supplementary Fig. 5a).…”

Section: Resultsmentioning

confidence: 99%

Extensive 5′-surveillance guards against non-canonical NAD-caps of nuclear mRNAs in yeast

et al. 2020

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The ubiquitous redox coenzyme nicotinamide adenine dinucleotide (NAD) acts as a non-canonical cap structure on prokaryotic and eukaryotic ribonucleic acids. Here we find that in budding yeast, NAD-RNAs are abundant (>1400 species), short (<170 nt), and mostly correspond to mRNA 5′-ends. The modification percentage of transcripts is low (<5%). NAD incorporation occurs mainly during transcription initiation by RNA polymerase II, which uses distinct promoters with a YAAG core motif for this purpose. Most NAD-RNAs are 3′-truncated. At least three decapping enzymes, Rai1, Dxo1, and Npy1, guard against NAD-RNA at different cellular locations, targeting overlapping transcript populations. NAD-mRNAs are not translatable in vitro. Our work indicates that in budding yeast, most of the NAD incorporation into RNA seems to be disadvantageous to the cell, which has evolved a diverse surveillance machinery to prematurely terminate, decap and reject NAD-RNAs.

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“…7b). When for those 25 genes all TSSs listed in the yeast TSS database 21 (top 5 abundant TSSs per gene) were analyzed, only a YA motif 22 was identified ( Supplementary Fig. 5a).…”

Section: Resultsmentioning

confidence: 99%

Extensive 5′-surveillance guards against non-canonical NAD-caps of nuclear mRNAs in yeast

et al. 2020

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“…The raw CAGE sequencing data generated in this study have been submitted to the NCBI BioProject database (BioProject; https:// www.ncbi.nlm.nih.gov/bioproject/) under accession number PRJNA483730. The quantitative maps of TSS and core promoters generated in this study can be visualized and downloaded from the YeasTSS database (http://www.yeastss.org) (McMillan et al 2019).…”

Section: Data Accessmentioning

confidence: 99%

Pervasive and dynamic transcription initiation in Saccharomyces cerevisiae

Lü

Zhang

2019

Genome Res.

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Transcription initiation is finely regulated to ensure proper expression and function of genes. The regulated transcription initiation in response to various environmental stimuli in a classic model organism Saccharomyces cerevisiae has not been systematically investigated. In this study, we generated quantitative maps of transcription start sites (TSSs) at a single-nucleotide resolution for S. cerevisiae grown in nine different conditions using no-amplification nontagging Cap analysis of gene expression (nAnT-iCAGE) sequencing. We mapped ∼1 million well-supported TSSs, suggesting highly pervasive transcription initiation in the compact genome of the budding yeast. The comprehensive TSS maps allowed us to identify core promoters for ∼96% verified protein-coding genes. We corrected misannotation of translation start codon for 122 genes and suggested an alternative start codon for 57 genes. We found that 56% of yeast genes are controlled by multiple core promoters, and alternative core promoter usage by a gene is widespread in response to changing environments. Most core promoter shifts are coupled with altered gene expression, indicating that alternative core promoter usage might play an important role in controlling gene transcriptional activities. Based on their activities in responding to environmental cues, we divided core promoters into constitutive class (55%) and inducible class (45%). The two classes of core promoters display distinctive patterns in transcriptional abundance, chromatin structure, promoter shape, and sequence context. In summary, our study improved the annotation of the yeast genome and demonstrated a much more pervasive and dynamic nature of transcription initiation in yeast than previously recognized.

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“…S1A). Genome-wide studies on the transcriptional start sites suggest that the second downstream ATG may be the actual start codon for SPL2 translation [37]. To further investigate the SPL2 start codon, we used promoter sequences corresponding to the annotated start codon, to the first downstream ATG and to the second downstream ATG.…”

Section: Spl2 Stimulates Its Own Expression and That Of Pho84mentioning

confidence: 99%

Cell-to-cell heterogeneity of phosphate gene expression in yeast is controlled by alternative transcription, 14-3-3 and Spl2

Crooijmans

Hensen

et al. 2021

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanism

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Dependent on phosphate availability the yeast Saccharomyces cerevisiae expresses either low or high affinity phosphate transporters. In the presence of phosphate yeast cells still express low levels of the high affinity phosphate transporter Pho84. The regulator Spl2 is expressed in approximately 90% of the cells, and is not expressed in the remaining cells. Here we report that deletion of RRP6, encoding an exonuclease degrading noncoding RNA, or BMH1, encoding the major 14-3-3 isoform, resulted in less cells expressing SPL2 and in increased levels of RNA transcribed from sequences upstream of the SPL2 coding region. SPL2 stimulates its own expression and that of PHO84 ensuing a positive feedback. Upon deletion of the region responsible for upstream SPL2 transcription almost all cells express SPL2. These results indicate that the cell-to-cell variation in PHO84 and SPL2 expression is dependent on a specific part of the SPL2 promoter and is controlled by Bmh1 and Spl2.

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YeasTSS: an integrative web database of yeast transcription start sites

Cited by 39 publications

References 68 publications

Extensive 5′-surveillance guards against non-canonical NAD-caps of nuclear mRNAs in yeast

Extensive 5′-surveillance guards against non-canonical NAD-caps of nuclear mRNAs in yeast

Pervasive and dynamic transcription initiation in Saccharomyces cerevisiae

Cell-to-cell heterogeneity of phosphate gene expression in yeast is controlled by alternative transcription, 14-3-3 and Spl2

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