---
res:
  bibo_abstract:
  - 'Biophysical constraints limit the specificity with which transcription factors
    (TFs) can target regulatory DNA. While individual nontarget binding events may
    be low affinity, the sheer number of such interactions could present a challenge
    for gene regulation by degrading its precision or possibly leading to an erroneous
    induction state. Chromatin can prevent nontarget binding by rendering DNA physically
    inaccessible to TFs, at the cost of energy-consuming remodeling orchestrated by
    pioneer factors (PFs). Under what conditions and by how much can chromatin reduce
    regulatory errors on a global scale? We use a theoretical approach to compare
    two scenarios for gene regulation: one that relies on TF binding to free DNA alone
    and one that uses a combination of TFs and chromatin-regulating PFs to achieve
    desired gene expression patterns. We find, first, that chromatin effectively silences
    groups of genes that should be simultaneously OFF, thereby allowing more accurate
    graded control of expression for the remaining ON genes. Second, chromatin buffers
    the deleterious consequences of nontarget binding as the number of OFF genes grows,
    permitting a substantial expansion in regulatory complexity. Third, chromatin-based
    regulation productively co-opts nontarget TF binding for ON genes in order to
    establish a “leaky” baseline expression level, which targeted activator or repressor
    binding subsequently up- or down-modulates. Thus, on a global scale, using chromatin
    simultaneously alleviates pressure for high specificity of regulatory interactions
    and enables an increase in genome size with minimal impact on global expression
    error.@eng'
  bibo_authorlist:
  - foaf_Person:
      foaf_givenName: Mindy Liu
      foaf_name: Perkins, Mindy Liu
      foaf_surname: Perkins
  - foaf_Person:
      foaf_givenName: Justin
      foaf_name: Crocker, Justin
      foaf_surname: Crocker
  - foaf_Person:
      foaf_givenName: Gašper
      foaf_name: Tkačik, Gašper
      foaf_surname: Tkačik
      foaf_workInfoHomepage: http://www.librecat.org/personId=3D494DCA-F248-11E8-B48F-1D18A9856A87
    orcid: 0000-0002-6699-1455
  bibo_doi: 10.1073/pnas.2411887121
  bibo_issue: '1'
  bibo_volume: 122
  dct_date: 2025^xs_gYear
  dct_identifier:
  - UT:001392765300001
  dct_isPartOf:
  - http://id.crossref.org/issn/0027-8424
  - http://id.crossref.org/issn/1091-6490
  dct_language: eng
  dct_publisher: National Academy of Sciences@
  dct_title: Chromatin enables precise and scalable gene regulation with factors of
    limited specificity@
  fabio_hasPubmedId: '39793086'
...