ArticleNature2024
Single-molecule states link transcription factor binding to gene expression.
Abstract read
In one paragraph
Article in Nature, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
0numbers the graph read from it
0cells of the map it votes in
32citing papers in PubMed
–field-weighted citation impact
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.
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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.
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Who cites it
32 citing papers in PubMed.
- Robust regulatory interplay of enhancers, facilitators, and promoters in a native chromatin context.Cell · 2026Article
- Exchange dynamics and kinetic control of gene regulation complexes.Nature reviews. Molecular cell biology · 2026Review
- A practical guide to studying genome function using single-molecule genomics.Nature reviews. Molecular cell biology · 2026Review
- Stable epigenetic states set single-cell activation thresholds in mammalian expression systems.bioRxiv : the preprint server for biology · 2026Article
- Cumulative transcription factor binding and p300-mediated histone acetylation drive enhancer activation frequency.Nature genetics · 2026Article
- Intrinsic promoter responsiveness dictates sensitivity to transcriptional activation by enhancers.bioRxiv : the preprint server for biology · 2026Article
- The Maximum Growth Temperature for Eukaryotes Is Thermodynamically Driven but Ecologically Contingent.Life (Basel, Switzerland) · 2026Article
- Article
- Graded versus ON/OFF control in quantitative gene expression and epigenetic memory.The EMBO journal · 2026Review
- Multi-scale dissection, compaction and derivatization of mammalian developmental enhancers.bioRxiv : the preprint server for biology · 2026Article
- Interplay between circadian and other transcription factors-Implications for cycling transcriptome reprogramming.FEBS letters · 2026Review
- Integrated analysis identifies conserved transcription factors TCF12, E2F1, and TEAD4 with diagnostic and therapeutic value in osteoarthritis subchondral bone.Genes & genomics · 2026Article
- Article
- Article
- The hypoxia-epigenetics-ncRNA axis in endometriosis: from molecular cascades to self-sustaining pathogenic circuits.Frontiers in endocrinology · 2026Review
- Bifunctional transcriptional effector domains control gene expression pulses in an occupancy-dependent manner.bioRxiv : the preprint server for biology · 2025Article
- A model of transcriptional bursting dynamics based on coupling between chromatin and enhancer states.bioRxiv : the preprint server for biology · 2025Article
- Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs.bioRxiv : the preprint server for biology · 2025Article
- FootprintCharter: unsupervised detection and quantification of footprints in single molecule footprinting data.Bioinformatics (Oxford, England) · 2025Article
- Coupling CRISPR scanning with targeted chromatin accessibility profiling using a double-stranded DNA deaminase.Nature methods · 2025Article
Corrections and comments
- Update of
Authors and funding
12 authors.
Benjamin R Doughty *Genetics Department, Stanford University, Stanford, CA, USA.ORCID 0000-0003-0447-4468
Michaela M Hinks *Bioengineering Department, Stanford University, Stanford, CA, USA.
Julia M Schaepe *Bioengineering Department, Stanford University, Stanford, CA, USA.ORCID 0000-0003-0416-0469
Georgi K MarinovGenetics Department, Stanford University, Stanford, CA, USA.ORCID 0000-0003-1822-7273
Abby R ThurmBiophysics Program, Stanford University, Stanford, CA, USA.ORCID 0000-0002-1819-3192
Carolina Rios-MartinezBioengineering Department, Stanford University, Stanford, CA, USA.
Benjamin E ParksComputer Science Department, Stanford University, Stanford, CA, USA.ORCID 0000-0002-0261-7472
Yingxuan TanComputer Science Department, Stanford University, Stanford, CA, USA.
Emil MarklundScience for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.ORCID 0000-0002-1150-7304
Danilo DubocaninGenetics Department, Stanford University, Stanford, CA, USA.
Lacramioara BintuBioengineering Department, Stanford University, Stanford, CA, USA. lbintu@stanford.edu.ORCID 0000-0001-5443-6633
William J GreenleafGenetics Department, Stanford University, Stanford, CA, USA. wjg@stanford.edu.ORCID 0000-0003-1409-3095
Funding
Special EquipmentP50HG007735 · NHGRI · STANFORD UNIVERSITY · PI SNYDER, MICHAEL P. · 2014 to 2018
$15.2MMedical Scientist Training ProgramT32GM145402 · NIGMS · STANFORD UNIVERSITY · PI Katrin F. Chua · 2022 to 2026
$10.0MHigh-throughput systematic characterization of regulatory element functionUM1HG009436 · NHGRI · STANFORD UNIVERSITY · PI BASSIK, MICHAEL C, GREENLEAF, WILLIAM JAMES · 2017 to 2021
$5.4MCombinatorial Cell State EngineeringDP1HG013599 · NHGRI · STANFORD UNIVERSITY · PI William James Greenleaf · 2023 to 2026
$5.4MSingle-cell analysis and synthetic control of mammalian chromatin dynamics and gene regulationR35GM128947 · NIGMS · STANFORD UNIVERSITY · PI Lacramioara Bintu · 2018 to 2026
$3.1MDefining and perturbing gene regulatory dynamics in the developing human brainR01NS128028 · NINDS · STANFORD UNIVERSITY · PI William James Greenleaf · 2023 to 2026
$2.4MDefining and perturbing gene regulatory dynamics in the developing human heart to understand mechanisms of congenital heart defectsR01HL171611 · NHLBI · STANFORD UNIVERSITY · PI William James Greenleaf · 2024 to 2026
$2.1MFast, powerful, scalable, usable, and distributable methods for multi-modal single cell analysesR01HG013317 · NHGRI · STANFORD UNIVERSITY · PI William James Greenleaf · 2024 to 2026
$2.1MNHGRI NIH HHS DP1 HG013599NHGRI NIH HHS P50 HG007735NHGRI NIH HHS R01 HG013317NHGRI NIH HHS UM1 HG009436NHLBI NIH HHS R01 HL171611NIGMS NIH HHS R35 GM128947NIGMS NIH HHS T32 GM145402NINDS NIH HHS R01 NS128028
Abstract
The binding of multiple transcription factors (TFs) to genomic enhancers drives gene expression in mammalian cells
Indexed as
Enhancer Elements, GeneticNucleosomesPromoter Regions, GeneticProtein BindingTranscription FactorsBinding SitesDNADNA FootprintingDNA MethylationGene Expression RegulationHumansInterferon Type IK562 CellsKineticsModels, MolecularResponse ElementsDNAInterferon Type INucleosomesTranscription Factors
Identifiers
What OpenQuestion holds
Textmetadata
LicenceTDM
Read underepoch 390
Registered trials
None linked
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.