ArticleGenetics2006
Gene expression from random libraries of yeast promoters.
Article in Genetics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 31 citations in OpenAlex.
- Next-generation stress-inducible Komagataella phaffii promoter variants.Microbial cell factories · 2025Article
- The development and characterization of synthetic minimal yeast promoters.Nature communications · 2015Article
- The grammar of transcriptional regulation.Human genetics · 2014Review
- Discrimination between thermodynamic models of cis-regulation using transcription factor occupancy data.Nucleic acids research · 2014Article
- Promoters maintain their relative activity levels under different growth conditions.Molecular systems biology · 2013Article
- Measurements of the impact of 3' end sequences on gene expression reveal wide range and sequence dependent effects.PLoS computational biology · 2013Article
- Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters.Nature biotechnology · 2012Article
- Compensation for differences in gene copy number among yeast ribosomal proteins is encoded within their promoters.Genome research · 2011Article
- Multiple sequence-specific factors generate the nucleosome-depleted region on CLN2 promoter.Molecular cell · 2011Article
- TATA is a modular component of synthetic promoters.Genome research · 2010Article
- Using DNA mechanics to predict in vitro nucleosome positions and formation energies.Nucleic acids research · 2009Article
- Incorporating nucleosomes into thermodynamic models of transcription regulation.Genome research · 2009Article
- Splicing of designer exons reveals unexpected complexity in pre-mRNA splicing.RNA (New York, N.Y.) · 2009Article
- DNA-binding properties of the yeast Rgt1 repressor.Biochimie · 2009Article
- Article
- A cis-regulatory logic simulator.BMC bioinformatics · 2007Article
- Enhancer responses to similarly distributed antagonistic gradients in development.PLoS computational biology · 2007Article
- Programming gene expression with combinatorial promoters.Molecular systems biology · 2007Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genomewide techniques to assay gene expression and transcription factor binding are in widespread use, but are far from providing predictive rules for the function of regulatory DNA. To investigate more intensively the grammar rules for active regulatory sequence, we made libraries from random ligations of a very restricted set of sequences. Working with the yeast Saccharomyces cerevisiae, we developed a novel screen based on the sensitivity of ascospores lacking dityrosine to treatment with lytic enzymes. We tested two separate libraries built by random ligation of a single type of activator site either for a well-characterized sporulation factor, Ndt80, or for a new sporulation-specific regulatory site that we identified and several neutral spacer elements. This selective system achieved up to 1:10(4) enrichment of the artificial sequences that were active during sporulation, allowing a high-throughput analysis of large libraries of synthetic promoters. This is not practical with methods involving direct screening for expression, such as those based on fluorescent reporters. There were very few false positives, since active promoters always passed the screen when retested. The survival rate of our libraries containing roughly equal numbers of spacers and activators was a few percent that of libraries made from activators alone. The sequences of approximately 100 examples of active and inactive promoters could not be distinguished by simple binary rules; instead, the best model for the data was a linear regression fit of a quantitative measure of gene activity to multiple features of the regulatory sequence.
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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.