{
  "abstract": "The CUT&Tag method performs exceptionally well for profiling histone modifications, but mapping sequence-specific transcription factors (TFs) is complicated by intrinsic Tn5 activity at accessible DNA, and the high-salt washes used to suppress this activity can destabilize TF-chromatin interactions. We engineered the Tn5 DNA-binding channel to attenuate target-DNA engagement by replacing individual positively charged amino acids with neutral amino acids. We identified a \"Goldilocks\" variant (K160A) with intermediate attenuation that improved recovery of GATA2 motif-containing sites under low-salt CUT&Tag and KCl-based DynaTag conditions. A second variant (K249A) had improved performance for profiling CTCF over less accessible sites characterized by sharply focused short-fragment enrichment. By comparing the K160A and K249A variants, this TF-CUT&Tag assay provides a physical readout of the local chromatin environment at TF binding sites. Applying K160A TF-CUT&Tag to pluripotency-associated TFs in mouse embryonic stem cells increased recovery across their genomic binding landscapes while preserving factor-specific motif architectures. During skeletal muscle differentiation, TF-CUT&Tag improved recovery of MyoG and Pax7 occupancy relative to standard CUT&Tag, revealing strongly motif-enriched MyoG binding and a shift in Pax7 binding from CpG-rich promoters in progenitors toward Pax7 motif-enriched sites during differentiation. Together, these results show that TF-CUT&Tag captures distinct modes of TF-chromatin interaction, including motif-directed binding sites and more salt-sensitive sites that may depend on lower-affinity DNA recognition or protein-protein interactions and are difficult to predict from DNA sequence alone.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 6,
  "authors": [
    {
      "name": "Lola Piper",
      "orcid": "0009-0002-4275-2385"
    },
    {
      "name": "Emma Baird",
      "orcid": "0009-0007-1002-7580"
    },
    {
      "name": "Harry J. Ashbaugh",
      "orcid": "0009-0000-8015-8331"
    },
    {
      "name": "Olivia A. Pentecost",
      "orcid": "0009-0003-7643-792X"
    },
    {
      "name": "Sara M. Nowinski",
      "orcid": "0000-0002-4744-6101"
    },
    {
      "name": "Derek H. Janssens",
      "orcid": "0000-0003-1079-9525"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/77bw32axwb7r6.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.10.27.762201",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.10.27.762201v1.full",
  "id": "77bw32axwb7r6",
  "issns": [
    "2692-8205"
  ],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.10.27.762201v1",
  "language": "en",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "genomics"
    ],
    [
      "heading",
      "Article"
    ],
    [
      "openalex",
      "1312|Genomics and Chromatin Dynamics"
    ]
  ],
  "openalex": "W7224125950",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.10.27.762201v1.full.pdf",
  "pmcid": "PMC13733980",
  "pmid": "42990448",
  "published": "2026-10-27",
  "publisher": "Cold Spring Harbor Laboratory Preprints",
  "ris": "https://research.draconitic.com/paper/77bw32axwb7r6.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:30:05Z",
      "native_id": "10.64898/2026.10.27.762201",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.10.27.762201v1"
    },
    {
      "first_seen": "2026-11-08T12:23:38Z",
      "native_id": "PMC13733980",
      "source": "pmc",
      "url": "https://doi.org/10.64898/2026.10.27.762201"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:genomics",
      "subfield": "genetics-genomics"
    }
  ],
  "title": "Engineered Tn5 Variants Enhance CUT&Tag Fidelity for Transcription Factors",
  "title_text": "Engineered Tn5 Variants Enhance CUT&Tag Fidelity for Transcription Factors",
  "type": "preprint",
  "updated_at": "2026-11-08T12:23:38Z",
  "url": "https://research.draconitic.com/paper/77bw32axwb7r6",
  "venue": "bioRxiv",
  "versions": []
}