ArticleGenome research2015
Core promoter sequence in yeast is a major determinant of expression level.
Article in Genome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed, 124 citations in OpenAlex.
- Dual-channel optogenetics in yeast for multiplexed light-based control of cellular processes and pathways.Nature communications · 2026Article
- Biological parts in yeast synthetic biology: from regulatory elements to predictive design platforms.FEMS yeast research · 2026Review
- Next-generation stress-inducible Komagataella phaffii promoter variants.Microbial cell factories · 2025Article
- De novo design of insulated cis-regulatory elements based on deep learning-predicted fitness landscape.Nucleic acids research · 2025Article
- Tuning fungal promoters for the expression of eukaryotic proteins.World journal of microbiology & biotechnology · 2024Review
- Proformer: a hybrid macaron transformer model predicts expression values from promoter sequences.BMC bioinformatics · 2024Article
- Review
- Quantitative analysis of transcription start site selection reveals control by DNA sequence, RNA polymerase II activity and NTP levels.Nature structural & molecular biology · 2024Article
- Review
- Combining TSS-MPRA and sensitive TSS profile dissimilarity scoring to study the sequence determinants of transcription initiation.Nucleic acids research · 2023Article
- Article
- Article
- Etiological roles of core promoter variation in triple-negative breast cancer.Genes & diseases · 2023Article
- Controlling gene expression with deep generative design of regulatory DNA.Nature communications · 2022Article
- Identification of enhancers responsible for the coordinated expression of myosin heavy chain isoforms in skeletal muscle.BMC genomics · 2022Article
- Transcriptional neighborhoods regulate transcript isoform lengths and expression levels.Science (New York, N.Y.) · 2022Article
- Engineering eukaryote-like regulatory circuits to expand artificial control mechanisms for metabolic engineering in Saccharomyces cerevisiae.Communications biology · 2022Article
- Large-scale analysis of Drosophila core promoter function using synthetic promoters.Molecular systems biology · 2022Article
- Performance of abiotic stress-inducible synthetic promoters in genetically engineered hybrid poplar (Frontiers in plant science · 2022Article
- Saccharomyces cerevisiae as a Heterologous Host for Natural Products.Methods in molecular biology (Clifton, N.J.) · 2022Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The core promoter is the regulatory sequence to which RNA polymerase is recruited and where it acts to initiate transcription. Here, we present the first comprehensive study of yeast core promoters, providing massively parallel measurements of core promoter activity and of TSS locations and relative usage for thousands of native and designed sequences. We found core promoter activity to be highly correlated to the activity of the entire promoter and that sequence variation in different core promoter regions substantially tunes its activity in a predictable way. We also show that location, orientation, and flanking bases critically affect TATA element function, that transcription initiation in highly active core promoters is focused within a narrow region, that poly(dA:dT) orientation has a functional consequence at the 3' end of promoters, and that orthologous core promoters across yeast species have conserved activities. Our results demonstrate the importance of core promoters in the quantitative study of gene regulation.
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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.