{"entity": "researcher", "timestamp": "2026-08-20T20:53:03.610Z", "family": "Crocker", "given": "Olivia J", "initials": "OJ", "orcid": "0000-0001-9249-6450", "affiliations": ["Genetics Department, Stanford University, Stanford, CA 94305, USA."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/0052fd29276f4ae2b5d1ee6afd063606.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/0052fd29276f4ae2b5d1ee6afd063606"}}, "publications": [{"entity": "publication", "iuid": "c43ff3561c8a40f6a435814334091283", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c43ff3561c8a40f6a435814334091283.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c43ff3561c8a40f6a435814334091283"}}, "title": "Thermodynamic principles link in vitro transcription factor affinities to single-molecule chromatin states in cells.", "authors": [{"family": "Schaepe", "given": "Julia M", "initials": "JM", "orcid": "0000-0003-0416-0469", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d029b6f8e7f346e098d7bef07a7d21a3.json"}}, {"family": "Fries", "given": "Torbj\u00f6rn", "initials": "T"}, {"family": "Doughty", "given": "Benjamin R", "initials": "BR", "orcid": "0000-0003-0447-4468", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4275613fa5cd43aca79c95189a33cd7d.json"}}, {"family": "Crocker", "given": "Olivia J", "initials": "OJ", "orcid": "0000-0001-9249-6450", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0052fd29276f4ae2b5d1ee6afd063606.json"}}, {"family": "Hinks", "given": "Michaela M", "initials": "MM", "orcid": "0009-0005-7918-3544", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/44ed10f5295e4cafa66790339b3f7c53.json"}}, {"family": "Marklund", "given": "Emil", "initials": "E", "orcid": "0000-0002-1150-7304", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a5e6f08a55df4af5927d91bf5f3f0870.json"}}, {"family": "Greenleaf", "given": "William J", "initials": "WJ", "orcid": "0000-0003-1409-3095", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ec47da61f6024af7b53412aadb7e6c8a.json"}}], "type": "journal article", "published": "2025-01-30", "journal": {"title": "bioRxiv", "issn": "2692-8205", "issn-l": null}, "abstract": "The molecular details governing transcription factor (TF) binding and the formation of accessible chromatin are not yet quantitatively understood - including how sequence context modulates affinity, how TFs search DNA, the kinetics of TF occupancy, and how motif grammars coordinate binding. To resolve these questions for a human TF, erythroid Kr\u00fcppel-like factor (eKLF/KLF1), we quantitatively compare, in high throughput, in vitro TF binding rates and affinities with in vivo single molecule TF and nucleosome occupancies across engineered DNA sequences. We find that 40-fold flanking sequence effects on affinity are consistent with distal flanks tuning TF search parameters and captured by a linear energy model. Motif recognition probability, rather than time in the bound state, drives affinity changes, and in vitro and in nuclei measurements exhibit consistent, minutes-long TF residence times. Finally, pairing in vitro biophysical parameters with thermodynamic models accurately predicts in vivo single-molecule chromatin states for unseen motif grammars.", "doi": "10.1101/2025.01.27.635162", "pmid": "39975040", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11838358"}, {"db": "pii", "key": "2025.01.27.635162"}], "notes": [], "created": "2026-08-20T11:00:42.016Z", "modified": "2026-08-20T11:00:42.185Z"}]}