ArticleNature biotechnology2012
Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters.
Article in Nature biotechnology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 298 papers, 1 of them a synthesis that pooled it.
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Who cites it
298 citing papers in PubMed, 1 synthesis or guideline pooled it, 523 citations in OpenAlex.
- Meta-analysis of massively parallel reporter assays enables prediction of regulatory function across cell types.Human mutation · 2019Pooled it
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- Synthetic Regulatory Genomics.Annual review of genomics and human genetics · 2026Review
- Do Genomic Patterns and Fibonacci-Like Regularity Hold the Key to Reproductive Fitness in Livestock?Biochemical genetics · 2026Article
- The adaptive landscapes of three globaleLife · 2026Article
- Decoding promoter activity from DNA sequence using pre-trained language models.Scientific reports · 2026Article
- Lentiviral single-cell MPRA of synthetic enhancers reveals motif affinity-based encoding of cell state specificity.Genome biology · 2026Article
- DNA Sequence Perplexity Reveals Evolutionarily Conserved Patterns in cis-Regulatory Regions Across Diverse Species.Biochemical genetics · 2026Article
- Informational blueprints reveal condition-dependent gene regulatory architectures.bioRxiv : the preprint server for biology · 2026Article
- PoolParty: streamlined design of DNA sequence libraries in Python.bioRxiv : the preprint server for biology · 2026Article
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- A mechanism of synergistic Mediator recruitment in RNA polymerase II transcription activation revealed by single-molecule fluorescence.Molecular cell · 2025Article
- Next-generation stress-inducible Komagataella phaffii promoter variants.Microbial cell factories · 2025Article
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- Predicting dynamic expression patterns in budding yeast with a fungal DNA language model.Research square · 2025Article
- Predicting dynamic expression patterns in budding yeast with a fungal DNA language model.bioRxiv : the preprint server for biology · 2025Article
- Highly efficient synthesis of the natural product β-himachalene in yeast and its potential as a novel anti-HSV-1 therapeutic agent.Synthetic and systems biotechnology · 2025Article
- Combinatorial Alkali-Responsive Hybrid Promoters as Tools for Heterologous Protein Expression in Saccharomyces cerevisiae.Microbial biotechnology · 2025Article
238 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors at 2 institutions in 2 countries.
Funding
Abstract
Despite extensive research, our understanding of the rules according to which cis-regulatory sequences are converted into gene expression is limited. We devised a method for obtaining parallel, highly accurate gene expression measurements from thousands of designed promoters and applied it to measure the effect of systematic changes in the location, number, orientation, affinity and organization of transcription-factor binding sites and nucleosome-disfavoring sequences. Our analyses reveal a clear relationship between expression and binding-site multiplicity, as well as dependencies of expression on the distance between transcription-factor binding sites and gene starts which are transcription-factor specific, including a striking ∼10-bp periodic relationship between gene expression and binding-site location. We show how this approach can measure transcription-factor sequence specificities and the sensitivity of transcription-factor sites to the surrounding sequence context, and compare the activity of 75 yeast transcription factors. Our method can be used to study both cis and trans effects of genotype on transcriptional, post-transcriptional and translational control.
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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.