ArticleMolecular cell2021
Molecular Co-occupancy Identifies Transcription Factor Binding Cooperativity In Vivo.
Article in Molecular cell, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 98 papers.
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
98 citing papers in PubMed, 169 citations in OpenAlex.
- A practical guide to studying genome function using single-molecule genomics.Nature reviews. Molecular cell biology · 2026Review
- Cumulative transcription factor binding and p300-mediated histone acetylation drive enhancer activation frequency.Nature genetics · 2026Article
- Intrinsic DNA codes govern distinct modes of nucleosome-transcription factor interactions.Nature communications · 2026Article
- Article
- Motif grammar and transcriptional programs decouple CTCF binding from nucleosome phasing to control cell-type-specific chromatin insulation.Cell reports · 2026Article
- Combinatorial pioneer transcription factor binding reinforces bivalent epigenetic states to preserve lineage fidelity.bioRxiv : the preprint server for biology · 2026Article
- Article
- Cardiac epigenome in heart development and disease.Nature reviews. Cardiology · 2026Review
- Interplay between circadian and other transcription factors-Implications for cycling transcriptome reprogramming.FEBS letters · 2026Review
- The ChIP-FRiP pipeline quantifies co-binding and reveals how antibody background contributes to cohesin ChIP-seq patterns.bioRxiv : the preprint server for biology · 2026Article
- High-resolution map of chromatin accessibility - insights into the focused binding of a large number of transcription factors.Epigenetics & chromatin · 2026Article
- Chromatin boundary permeability is controlled by CTCF conformational ensembles.bioRxiv : the preprint server for biology · 2026Article
- The role of cohesin loading at enhancers in the flux of loop extrusion and long-range transcriptional control.bioRxiv : the preprint server for biology · 2026Article
- Deciphering the regulatory landscape of enhancer RNAs in health and disease.Signal transduction and targeted therapy · 2026Review
- Article
- ChromTag: an interactive R-shiny platform for analysis and visualization of CUT&Tag and ChIP-seq peak profiling data.Frontiers in bioinformatics · 2026Article
- Single-nucleus multiomics reveals the disrupted regulatory programs in three brain regions of sporadic early-onset Alzheimer's disease.Science advances · 2025Article
- Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs.bioRxiv : the preprint server for biology · 2025Article
- Genome-wide investigation of transcription factor footprints and dynamics using cFOOT-seq.Protein & cell · 2025Article
- FootprintCharter: unsupervised detection and quantification of footprints in single molecule footprinting data.Bioinformatics (Oxford, England) · 2025Article
38 more citing papers are in PubMed but not listed here.
Corrections and comments
- Commented on by
Authors and funding
9 authors at 7 institutions in 4 countries.
Funding
Abstract
Gene activation requires the cooperative activity of multiple transcription factors at cis-regulatory elements (CREs). Yet, most transcription factors have short residence time, questioning the requirement of their physical co-occupancy on DNA to achieve cooperativity. Here, we present a DNA footprinting method that detects individual molecular interactions of transcription factors and nucleosomes with DNA in vivo. We apply this strategy to quantify the simultaneous binding of multiple transcription factors on single DNA molecules at mouse CREs. Analysis of the binary occupancy patterns at thousands of motif combinations reveals that high DNA co-occupancy occurs for most types of transcription factors, in the absence of direct physical interaction, at sites of competition with nucleosomes. Perturbation of pairwise interactions demonstrates the function of molecular co-occupancy in binding cooperativity. Our results reveal the interactions regulating CREs at molecular resolution and identify DNA co-occupancy as a widespread cooperativity mechanism used by transcription factors to remodel chromatin.
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.