ArticleeLife2019
Determining cellular CTCF and cohesin abundances to constrain 3D genome models.
Article in eLife, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 94 papers.
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94 citing papers in PubMed, 162 citations in OpenAlex.
- A scaffolding element rewires local 3D chromatin architecture during differentiation.Nature communications · 2026Article
- Genome-wide absolute quantification of chromatin looping.Nature structural & molecular biology · 2026Article
- Combinatorial pioneer transcription factor binding reinforces bivalent epigenetic states to preserve lineage fidelity.bioRxiv : the preprint server for biology · 2026Article
- Cohesin bridging as a physical principle of enhancer-promoter communication.bioRxiv : the preprint server for biology · 2026Article
- Cohesin cofactor dosage sets the rate of loop extrusion, rendering genome folding tunable yet vulnerable to genetic disruption.Molecular cell · 2026Article
- Organization of replicated chromosomes by DNA loops and sister chromatid cohesion.Nature reviews. Molecular cell biology · 2026Review
- A universal polymer signature in Hi-C resolves cohesin loop density and supports monomeric extrusion.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- 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
- 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
- Single-molecule tracking of DNMT1 in living cells reveals its cell cycle dynamics and its redistribution upon drug treatment.Nucleic acids research · 2026Article
- Uniform dynamics of cohesin-mediated loop extrusion in living human cells.Nature genetics · 2025Article
- A molecular census to elucidate the demixing mechanism of membraneless organelles.Genome biology · 2025Article
- Dosage sensitivity of the loop extrusion rate confers tunability to genome folding while creating vulnerability to genetic disruption.bioRxiv : the preprint server for biology · 2025Article
- RETRACTED: Kinetic organization of the genome revealed by ultraresolution multiscale live imaging.Science (New York, N.Y.) · 2025Article
- Single-molecule live imaging of subunit interactions and exchange within cellular regulatory complexes.Molecular cell · 2025Article
- Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy.Genome research · 2025Article
- Master transcription-factor binding sites constitute the core of early replication control elements.The EMBO journal · 2025Article
- Deletion of a single CTCF motif at the boundary of a chromatin domain with three FGF genes disrupts gene expression and embryonic development.Developmental cell · 2025Article
- CTCF binding landscape is shaped by the epigenetic state of the N-terminal nucleosome in relation to CTCF motif orientation.Nucleic acids research · 2025Article
- High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion.Nature communications · 2025Article
34 more citing papers are in PubMed but not listed here.
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12 authors at 3 institutions in 2 countries.
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Abstract
Achieving a quantitative and predictive understanding of 3D genome architecture remains a major challenge, as it requires quantitative measurements of the key proteins involved. Here, we report the quantification of CTCF and cohesin, two causal regulators of topologically associating domains (TADs) in mammalian cells. Extending our previous imaging studies (Hansen et al., 2017), we estimate bounds on the density of putatively DNA loop-extruding cohesin complexes and CTCF binding site occupancy. Furthermore, co-immunoprecipitation studies of an endogenously tagged subunit (Rad21) suggest the presence of cohesin dimers and/or oligomers. Finally, based on our cell lines with accurately measured protein abundances, we report a method to conveniently determine the number of molecules of any Halo-tagged protein in the cell. We anticipate that our results and the established tool for measuring cellular protein abundances will advance a more quantitative understanding of 3D genome organization, and facilitate protein quantification, key to comprehend diverse biological processes.
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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.