ArticleeLife2019
Negative reciprocity, not ordered assembly, underlies the interaction of Sox2 and Oct4 on DNA.
Article in eLife, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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.
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Who cites it
20 citing papers in PubMed, 42 citations in OpenAlex.
- Algebraic formulas for first-passage times of Markov processes in the linear framework.Bulletin of mathematical biology · 2025Article
- Emergence of activation or repression in transcriptional control under a fixed molecular context.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- GenomicLayers: sequence-based simulation of epi-genomes.BMC bioinformatics · 2025Article
- Emerging cooperativity between Oct4 and Sox2 governs the pluripotency network in early mouse embryos.eLife · 2025Article
- Governing principles of transcriptional logic out of equilibrium.Biophysical journal · 2024Article
- Transcriptional kinetic synergy: A complex landscape revealed by integrating modeling and synthetic biology.Cell systems · 2023Article
- Competing constraints shape the nonequilibrium limits of cellular decision-making.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- The linear framework II: using graph theory to analyse the transient regime of Markov processes.Frontiers in cell and developmental biology · 2023Article
- Article
- Pioneer Factor Improves CRISPR-Based C-To-G and C-To-T Base Editing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2022Article
- The linear framework: using graph theory to reveal the algebra and thermodynamics of biomolecular systems.Interface focus · 2022Review
- Oct4 differentially regulates chromatin opening and enhancer transcription in pluripotent stem cells.eLife · 2022Article
- Pluripotency factors determine gene expression repertoire at zygotic genome activation.Nature communications · 2022Article
- Review
- The needle and the haystack: single molecule tracking to probe the transcription factor search in eukaryotes.Biochemical Society transactions · 2021Review
- Altering transcription factor binding reveals comprehensive transcriptional kinetics of a basic gene.Nucleic acids research · 2021Article
- Allosteric conformational ensembles have unlimited capacity for integrating information.eLife · 2021Article
- Single-molecule tracking of transcription protein dynamics in living cells: seeing is believing, but what are we seeing?Current opinion in genetics & development · 2021Review
- Article
- Nonreciprocal and Conditional Cooperativity Directs the Pioneer Activity of Pluripotency Transcription Factors.Cell reports · 2019Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The mode of interaction of transcription factors (TFs) on eukaryotic genomes remains a matter of debate. Single-molecule data in living cells for the TFs Sox2 and Oct4 were previously interpreted as evidence of ordered assembly on DNA. However, the quantity that was calculated does not determine binding order but, rather, energy expenditure away from thermodynamic equilibrium. Here, we undertake a rigorous biophysical analysis which leads to the concept of reciprocity. The single-molecule data imply that Sox2 and Oct4 exhibit negative reciprocity, with expression of Sox2 increasing Oct4's genomic binding but expression of Oct4 decreasing Sox2's binding. Models show that negative reciprocity can arise either from energy expenditure or from a mixture of positive and negative cooperativity at distinct genomic loci. Both possibilities imply unexpected complexity in how TFs interact on DNA, for which single-molecule methods provide novel detection capabilities.
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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.