High throughput screening identifies SOX2 as a super pioneer factor that inhibits DNA methylation maintenance at its binding sites

Nat Commun. 2021 Jun 7;12(1):3337. doi: 10.1038/s41467-021-23630-x.

Abstract

Binding of mammalian transcription factors (TFs) to regulatory regions is hindered by chromatin compaction and DNA methylation of their binding sites. Nevertheless, pioneer transcription factors (PFs), a distinct class of TFs, have the ability to access nucleosomal DNA, leading to nucleosome remodelling and enhanced chromatin accessibility. Whether PFs can bind to methylated sites and induce DNA demethylation is largely unknown. Using a highly parallelized approach to investigate PF ability to bind methylated DNA and induce DNA demethylation, we show that the interdependence between DNA methylation and TF binding is more complex than previously thought, even within a select group of TFs displaying pioneering activity; while some PFs do not affect the methylation status of their binding sites, we identified PFs that can protect DNA from methylation and others that can induce DNA demethylation at methylated binding sites. We call the latter super pioneer transcription factors (SPFs), as they are seemingly able to overcome several types of repressive epigenetic marks. Finally, while most SPFs induce TET-dependent active DNA demethylation, SOX2 binding leads to passive demethylation, an activity enhanced by the co-binding of OCT4. This finding suggests that SPFs could interfere with epigenetic memory during DNA replication.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Binding Sites*
  • Chromatin
  • DNA / metabolism*
  • DNA Demethylation
  • DNA Methylation*
  • DNA Replication
  • Epigenomics
  • Gene Expression
  • High-Throughput Screening Assays*
  • Mice
  • Nucleosomes
  • Octamer Transcription Factor-3 / metabolism
  • Protein Binding
  • RNA, Small Interfering / genetics
  • SOXB1 Transcription Factors / genetics*
  • SOXB1 Transcription Factors / metabolism*
  • Sf9 Cells
  • Transcription Factors / metabolism

Substances

  • Chromatin
  • Nucleosomes
  • Octamer Transcription Factor-3
  • POU5F1 protein, human
  • RNA, Small Interfering
  • SOX2 protein, human
  • SOXB1 Transcription Factors
  • Transcription Factors
  • DNA

Associated data

  • figshare/10.6084/m9.figshare.7087697