ArticleGenome research2013
Massively parallel synthetic promoter assays reveal the in vivo effects of binding site variants.
Article in Genome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers, 1 of them a synthesis that pooled it.
What it found
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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
71 citing papers in PubMed, 1 synthesis or guideline pooled it, 113 citations in OpenAlex.
- Meta-analysis of massively parallel reporter assays enables prediction of regulatory function across cell types.Human mutation · 2019Pooled it
- Gaugefixer: overcoming parameter non-identifiability in models of sequence-function relationships.BMC bioinformatics · 2026Article
- Expression-linked promoter selection (ELiPS) engineers short, strong ubiquitous promoters for gene therapy applications.bioRxiv : the preprint server for biology · 2026Article
- GaugeFixer: overcoming parameter non-identifiability in models of sequence-function relationships.bioRxiv : the preprint server for biology · 2026Article
- PoolParty: streamlined design of DNA sequence libraries in Python.bioRxiv : the preprint server for biology · 2026Article
- Gauge fixing for sequence-function relationships.PLoS computational biology · 2025Article
- MoCHI: neural networks to fit interpretable models and quantify energies, energetic couplings, epistasis, and allostery from deep mutational scanning data.Genome biology · 2024Article
- Review
- Decoding biology with massively parallel reporter assays and machine learning.Genes & development · 2024Review
- Generating information-dense promoter sequences with optimal string packing.PLoS computational biology · 2024Article
- Gauge fixing for sequence-function relationships.bioRxiv : the preprint server for biology · 2024Article
- Optimizing sequence design strategies for perturbation MPRAs: a computational evaluation framework.Nucleic acids research · 2024Article
- Proformer: a hybrid macaron transformer model predicts expression values from promoter sequences.BMC bioinformatics · 2024Article
- Transcription factor interactions explain the context-dependent activity of CRX binding sites.PLoS computational biology · 2024Article
- Review
- Precision engineering of biological function with large-scale measurements and machine learning.PloS one · 2023Article
- Multiplexed functional genomic assays to decipher the noncoding genome.Human molecular genetics · 2022Article
- Systematic analysis of low-affinity transcription factor binding site clusters in vitro and in vivo establishes their functional relevance.Nature communications · 2022Article
- A synthetic synthesis to explore animal evolution and development.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Review
- MAVE-NN: learning genotype-phenotype maps from multiplex assays of variant effect.Genome biology · 2022Article
11 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
3 authors at 1 institution in 1 country.
Funding
Abstract
Gene promoters typically contain multiple transcription factor binding sites (TFBSs), which may vary in affinity for their cognate transcription factors (TFs). One major challenge in studying cis-regulation is to understand how TFBS variants affect gene expression. We studied the in vivo effects of TFBS variants on cis-regulation using synthetic promoters coupled with a thermodynamic model of TF binding. We measured expression driven by each promoter with RNA-seq of transcribed sequence barcodes. This allowed reporter genes to be highly multiplexed and increased our statistical power to detect the effects of TFBS variants. We analyzed the effects of TFBS variants using a thermodynamic framework that models both TF-DNA interactions and TF-TF interactions. We found that this system accurately estimates the in vivo relative affinities of TFBSs and predicts unexpected interactions between several TFBSs. Our results reveal that binding site variants can have complex effects on gene expression due to differences in TFBS affinity for cognate TFs and differences in TFBS specificity for noncognate TFs.
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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.