STAG2 mutations alter CTCF-anchored loop extrusion, reduce cis-regulatory interactions and EWSR1-FLI1 activity in Ewing sarcoma

Cancer Cell. 2021 Jun 14;39(6):810-826.e9. doi: 10.1016/j.ccell.2021.04.001. Epub 2021 Apr 29.


STAG2, a cohesin family gene, is among the most recurrently mutated genes in cancer. STAG2 loss of function (LOF) is associated with aggressive behavior in Ewing sarcoma, a childhood cancer driven by aberrant transcription induced by the EWSR1-FLI1 fusion oncogene. Here, using isogenic Ewing cells, we show that, while STAG2 LOF profoundly changes the transcriptome, it does not significantly impact EWSR1-FLI1, CTCF/cohesin, or acetylated H3K27 DNA binding patterns. In contrast, it strongly alters the anchored dynamic loop extrusion process at boundary CTCF sites and dramatically decreases promoter-enhancer interactions, particularly affecting the expression of genes regulated by EWSR1-FLI1 at GGAA microsatellite neo-enhancers. Down-modulation of cis-mediated EWSR1-FLI1 activity, observed in STAG2-LOF conditions, is associated with enhanced migration and invasion properties of Ewing cells previously observed in EWSR1-FLI1low cells. Our study illuminates a process whereby STAG2-LOF fine-tunes the activity of an oncogenic transcription factor through altered CTCF-anchored loop extrusion and cis-mediated enhancer mechanisms.

Keywords: CTCF; Ewing sarcoma; STAG1; STAG2; anchorage; chromatin extrusion; cohesin; enhancer; loop; migration.

Publication types

  • Research Support, Non-U.S. Gov't
  • Video-Audio Media

MeSH terms

  • Bone Neoplasms / genetics*
  • Bone Neoplasms / mortality
  • Bone Neoplasms / pathology
  • CCCTC-Binding Factor / chemistry
  • CCCTC-Binding Factor / genetics
  • CCCTC-Binding Factor / metabolism*
  • Cell Cycle Proteins / genetics*
  • Cell Cycle Proteins / metabolism
  • Cell Line, Tumor
  • Cell Movement / genetics
  • Chromatin Immunoprecipitation
  • Chromosomal Proteins, Non-Histone / metabolism
  • Cohesins
  • Enhancer Elements, Genetic
  • Gene Expression Regulation, Neoplastic
  • Histones / metabolism
  • Humans
  • Loss of Function Mutation
  • Lysine / metabolism
  • Oncogene Proteins, Fusion / genetics*
  • Oncogene Proteins, Fusion / metabolism
  • Promoter Regions, Genetic
  • Sarcoma, Ewing / genetics*
  • Sarcoma, Ewing / mortality
  • Sarcoma, Ewing / pathology


  • CCCTC-Binding Factor
  • CTCF protein, human
  • Cell Cycle Proteins
  • Chromosomal Proteins, Non-Histone
  • EWSR1-FLI1 fusion protein, human
  • Histones
  • Oncogene Proteins, Fusion
  • STAG2 protein, human
  • Lysine