ArticleNature genetics2013
Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model.
Article in Nature genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 162 papers, 2 of them syntheses that pooled it.
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
162 citing papers in PubMed, 2 syntheses or guidelines pooled it, 259 citations in OpenAlex.
- Meta-analysis of massively parallel reporter assays enables prediction of regulatory function across cell types.Human mutation · 2019Pooled it
- Gene regulatory mechanisms underpinning prostate cancer susceptibility.Nature genetics · 2016Pooled it
- Robust regulatory interplay of enhancers, facilitators, and promoters in a native chromatin context.Cell · 2026Article
- Unlocking the Regulatory Genome: Interpreting the Clinical Impact of Noncoding Variants in Genetic Cardiomyopathies.Circulation. Genomic and precision medicine · 2026Review
- Article
- Multi-scale dissection, compaction and derivatization of mammalian developmental enhancers.bioRxiv : the preprint server for biology · 2026Article
- PoolParty: streamlined design of DNA sequence libraries in Python.bioRxiv : the preprint server for biology · 2026Article
- Transcription factors Lef1 and Rest stimulate recovery from depressive states.Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2026Article
- Mechanisms of enhanced or impaired DNA target selectivity driven by protein dimerization.PNAS nexus · 2026Article
- Review
- Simultaneous epigenomic profiling and regulatory activity measurement using e2MPRA.Nature communications · 2026Article
- Identification of novel DNA sequence motifs that modulate transcription in T cells.BMC genomics · 2026Article
- Synthetic promoters developed through a site-specific integration system enhance antibody expression in fed-batch culture.Engineering in life sciences · 2026Article
- Motif-based models accurately predict cell type-specific distal regulatory elements.Nature communications · 2025Article
- Deep learning the dynamic regulatory sequence code of cardiac organoid differentiation.bioRxiv : the preprint server for biology · 2025Article
- Massively parallel reporter assay reveals promoter-, position-, and strand-specific effects in transcription start sites.bioRxiv : the preprint server for biology · 2025Article
- Mechanisms of enhanced or impaired DNA target selectivity driven by protein dimerization.bioRxiv : the preprint server for biology · 2025Article
- Article
- Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity.Nature communications · 2025Article
- Article
102 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
8 authors at 3 institutions in 2 countries.
Funding
Abstract
Despite continual progress in the cataloging of vertebrate regulatory elements, little is known about their organization and regulatory architecture. Here we describe a massively parallel experiment to systematically test the impact of copy number, spacing, combination and order of transcription factor binding sites on gene expression. A complex library of ∼5,000 synthetic regulatory elements containing patterns from 12 liver-specific transcription factor binding sites was assayed in mice and in HepG2 cells. We find that certain transcription factors act as direct drivers of gene expression in homotypic clusters of binding sites, independent of spacing between sites, whereas others function only synergistically. Heterotypic enhancers are stronger than their homotypic analogs and favor specific transcription factor binding site combinations, mimicking putative native enhancers. Exhaustive testing of binding site permutations suggests that there is flexibility in binding site order. Our findings provide quantitative support for a flexible model of regulatory element activity and suggest a framework for the design of synthetic tissue-specific enhancers.
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.