ArticleProceedings of the National Academy of Sciences of the United States of America2006
A large-scale full-length cDNA analysis to explore the budding yeast transcriptome.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 142 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
142 citing papers in PubMed, 235 citations in OpenAlex.
- Genetic dissection of transcription start site selection by RNA polymerase II in Saccharomyces cerevisiae.Genetics · 2026Article
- Genetic dissection of transcription start site selection by RNA Polymerase II inbioRxiv : the preprint server for biology · 2025Article
- Identification and Functions of lncRNAs in Fungi.Non-coding RNA · 2025Review
- Identification of translation events that drive nonsense-mediated mRNA decay reveals functional roles for noncoding RNAs.bioRxiv : the preprint server for biology · 2025Article
- Pleiotropic effects of PAB1 deletion: Extensive changes in the yeast proteome, transcriptome, and translatome.PLoS genetics · 2024Article
- Extended stop codon context predicts nonsense codon readthrough efficiency in human cells.Nature communications · 2024Article
- Interaction of the La-related protein Slf1 with colliding ribosomes maintains translation of oxidative-stress responsive mRNAs.Nucleic acids research · 2023Article
- Impact of uORFs in mediating regulation of translation in stress conditions.BMC molecular and cell biology · 2021Article
- High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts.Genome biology · 2021Article
- Alternative transcription start sites of the enolase-encoding gene enoA are stringently used in glycolytic/gluconeogenic conditions in Aspergillus oryzae.Current genetics · 2020Article
- Transcriptome visualization and data availability at the Saccharomyces Genome Database.Nucleic acids research · 2020Article
- GCN sensitive protein translation in yeast.PloS one · 2020Article
- Control of Translation at the Initiation Phase During Glucose Starvation in Yeast.International journal of molecular sciences · 2019Review
- Rapidly evolving protointrons in Saccharomyces genomes revealed by a hungry spliceosome.PLoS genetics · 2019Article
- Pervasive and dynamic transcription initiation inGenome research · 2019Article
- Translatome and transcriptome analysis of TMA20 (MCT-1) and TMA64 (eIF2D) knockout yeast strains.Data in brief · 2019Article
- Completion of the cytosolic post-chorismate phenylalanine biosynthetic pathway in plants.Nature communications · 2019Article
- Dynamics of Chromatin and Transcription during Transient Depletion of the RSC Chromatin Remodeling Complex.Cell reports · 2019Article
- YeasTSS: an integrative web database of yeast transcription start sites.Database : the journal of biological databases and curation · 2019Article
- The Contribution of Purifying Selection, Linkage, and Mutation Bias to the Negative Correlation between Gene Expression and Polymorphism Density in Yeast Populations.Genome biology and evolution · 2018Article
82 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We performed a large-scale cDNA analysis to explore the transcriptome of the budding yeast Saccharomyces cerevisiae. We sequenced two cDNA libraries, one from the cells exponentially growing in a minimal medium and the other from meiotic cells. Both libraries were generated by using a vector-capping method that allows the accurate mapping of transcription start sites (TSSs). Consequently, we identified 11,575 TSSs associated with 3,638 annotated genomic features, including 3,599 ORFs, to suggest that most yeast genes have two or more TSSs. In addition, we identified 45 previously undescribed introns, including those affecting current ORF annotations and those spliced alternatively. Furthermore, the analysis revealed 667 transcription units in the intergenic regions and transcripts derived from antisense strands of 367 known features. We also found that 348 ORFs carry TSSs in their 3'-halves to generate sense transcripts starting from inside the ORFs. These results indicate that the budding yeast transcriptome is considerably more complex than previously thought, and it shares many recently revealed characteristics with the transcriptomes of mammals and other higher eukaryotes. Thus, the genome-wide active transcription that generates novel classes of transcripts appears to be an intrinsic feature of the eukaryotic cells. The budding yeast will serve as a versatile model for the studies on these aspects of transcriptome, and the full-length cDNA clones can function as an invaluable resource in such studies.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.