Synthetic regulatory genomics uncovers enhancer context dependence at the Sox2 locus

Ran Brosh, Camila Coelho, André M. Ribeiro-dos-Santos, Gwen Ellis, Megan S. Hogan, Hannah J. Ashe, Nicolette Somogyi, Raquel Ordoñez, Raven D. Luther, Emily Huang, Jef D. Boeke, Matthew T. Maurano

Research output: Contribution to journalArticlepeer-review


Sox2 expression in mouse embryonic stem cells (mESCs) depends on a distal cluster of DNase I hypersensitive sites (DHSs), but their individual contributions and degree of interdependence remain a mystery. We analyzed the endogenous Sox2 locus using Big-IN to scarlessly integrate large DNA payloads incorporating deletions, rearrangements, and inversions affecting single or multiple DHSs, as well as surgical alterations to transcription factor (TF) recognition sequences. Multiple mESC clones were derived for each payload, sequence-verified, and analyzed for Sox2 expression. We found that two DHSs comprising a handful of key TF recognition sequences were each sufficient for long-range activation of Sox2 expression. By contrast, three nearby DHSs were entirely context dependent, showing no activity alone but dramatically augmenting the activity of the autonomous DHSs. Our results highlight the role of context in modulating genomic regulatory element function, and our synthetic regulatory genomics approach provides a roadmap for the dissection of other genomic loci.

Original languageEnglish (US)
Pages (from-to)1140-1152.e7
JournalMolecular Cell
Issue number7
StatePublished - Apr 6 2023


  • CTCF
  • enhancers
  • gene regulation
  • genetic engineering
  • genome writing
  • stem cells
  • synthetic regulatory genomics

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology


Dive into the research topics of 'Synthetic regulatory genomics uncovers enhancer context dependence at the Sox2 locus'. Together they form a unique fingerprint.

Cite this