Systematic identification of factors for provirus silencing in embryonic stem cells

Cell. 2015 Sep 24;163(1):230-45. doi: 10.1016/j.cell.2015.08.037. Epub 2015 Sep 10.


Embryonic stem cells (ESCs) repress the expression of exogenous proviruses and endogenous retroviruses (ERVs). Here, we systematically dissected the cellular factors involved in provirus repression in embryonic carcinomas (ECs) and ESCs by a genome-wide siRNA screen. Histone chaperones (Chaf1a/b), sumoylation factors (Sumo2/Ube2i/Sae1/Uba2/Senp6), and chromatin modifiers (Trim28/Eset/Atf7ip) are key determinants that establish provirus silencing. RNA-seq analysis uncovered the roles of Chaf1a/b and sumoylation modifiers in the repression of ERVs. ChIP-seq analysis demonstrates direct recruitment of Chaf1a and Sumo2 to ERVs. Chaf1a reinforces transcriptional repression via its interaction with members of the NuRD complex (Kdm1a, Hdac1/2) and Eset, while Sumo2 orchestrates the provirus repressive function of the canonical Zfp809/Trim28/Eset machinery by sumoylation of Trim28. Our study reports a genome-wide atlas of functional nodes that mediate proviral silencing in ESCs and illuminates the comprehensive, interconnected, and multi-layered genetic and epigenetic mechanisms by which ESCs repress retroviruses within the genome.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Chromatin Assembly Factor-1 / genetics
  • Chromatin Assembly Factor-1 / metabolism
  • Embryonal Carcinoma Stem Cells / virology
  • Embryonic Stem Cells / virology*
  • Endogenous Retroviruses / genetics*
  • Epigenesis, Genetic
  • Mice
  • Proviruses / genetics*
  • Small Ubiquitin-Related Modifier Proteins / metabolism


  • Chaf1a protein, mouse
  • Chaf1b protein, mouse
  • Chromatin Assembly Factor-1
  • Small Ubiquitin-Related Modifier Proteins

Associated data

  • GEO/GSE70865