A genome-wide RNAi screen identifies a new transcriptional module required for self-renewal

Genes Dev. 2009 Apr 1;23(7):837-48. doi: 10.1101/gad.1769609.


We performed a genome-wide siRNA screen in mouse embryonic stem (ES) cells to identify genes essential for self-renewal, and found 148 genes whose down-regulation caused differentiation. Many of the identified genes function in gene regulation and/or development, and are highly expressed in ES cells and embryonic tissues. We further identified target genes of two transcription regulators Cnot3 and Trim28. We discovered that Cnot3 and Trim28 co-occupy many putative gene promoters with c-Myc and Zfx, but not other pluripotency-associated transcription factors. They form a unique module in the self-renewal transcription network, separate from the core module formed by Nanog, Oct4, and Sox2. The transcriptional targets of this module are enriched for genes involved in cell cycle, cell death, and cancer. This supports the idea that regulatory networks controlling self-renewal in stem cells may also be active in certain cancers and may represent novel anti-cancer targets. Our screen has implicated over 100 new genes in ES cell self-renewal, and illustrates the power of RNAi and forward genetics for the systematic study of self-renewal.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Differentiation*
  • Cells, Cultured
  • DNA-Binding Proteins / metabolism
  • Embryonic Stem Cells / cytology*
  • Gene Expression Profiling
  • Gene Expression Regulation, Developmental
  • Gene Silencing
  • Genome / genetics*
  • Kruppel-Like Transcription Factors / metabolism
  • Mice
  • Neoplasms / physiopathology
  • Nuclear Proteins / metabolism
  • RNA Interference*
  • RNA, Small Interfering / genetics
  • Repressor Proteins / metabolism
  • Reproducibility of Results
  • Salivary alpha-Amylases
  • Transcription Factors / metabolism
  • Tripartite Motif-Containing Protein 28


  • DNA-Binding Proteins
  • Kruppel-Like Transcription Factors
  • Nuclear Proteins
  • RNA, Small Interfering
  • Repressor Proteins
  • Transcription Factors
  • zinc finger protein, X-linked
  • Trim28 protein, mouse
  • Tripartite Motif-Containing Protein 28
  • Amy1 protein, mouse
  • Salivary alpha-Amylases