Activation of a T-box-Otx2-Gsc gene network independent of TBP and TBP-related factors

Development. 2016 Apr 15;143(8):1340-50. doi: 10.1242/dev.127936. Epub 2016 Mar 7.


Embryonic development relies on activating and repressing regulatory influences that are faithfully integrated at the core promoter of individual genes. In vertebrates, the basal machinery recognizing the core promoter includes TATA-binding protein (TBP) and two TBP-related factors. In Xenopus embryos, the three TBP family factors are all essential for development and are required for expression of distinct subsets of genes. Here, we report on a non-canonical TBP family-insensitive (TFI) mechanism of transcription initiation that involves mesoderm and organizer gene expression. Using TBP family single- and triple-knockdown experiments, α-amanitin treatment, transcriptome profiling and chromatin immunoprecipitation, we found that TFI gene expression cannot be explained by functional redundancy, is supported by active transcription and shows normal recruitment of the initiating form of RNA polymerase II to the promoter. Strikingly, recruitment of Gcn5 (also known as Kat2a), a co-activator that has been implicated in transcription initiation, to TFI gene promoters is increased upon depletion of TBP family factors. TFI genes are part of a densely connected TBP family-insensitive T-box-Otx2-Gsc interaction network. The results indicate that this network of genes bound by Vegt, Eomes, Otx2 and Gsc utilizes a novel, flexible and non-canonical mechanism of transcription that does not require TBP or TBP-related factors.

Keywords: Gene regulation; Mesoderm; Organizer; TATA-binding protein; Xenopus.

Publication types

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

MeSH terms

  • Animals
  • Gastrulation
  • Gene Expression Regulation, Developmental*
  • Gene Knockdown Techniques
  • Gene Regulatory Networks*
  • Goosecoid Protein / genetics*
  • Histone Acetyltransferases / metabolism
  • Otx Transcription Factors / genetics*
  • Otx Transcription Factors / metabolism
  • Protein Binding
  • TATA Box Binding Protein-Like Proteins / genetics
  • TATA-Box Binding Protein / metabolism*
  • Transcription Initiation, Genetic*
  • Xenopus
  • Xenopus Proteins / genetics*
  • Xenopus Proteins / metabolism


  • Goosecoid Protein
  • Otx Transcription Factors
  • Otx2 protein, Xenopus
  • TATA Box Binding Protein-Like Proteins
  • TATA-Box Binding Protein
  • Xenopus Proteins
  • Histone Acetyltransferases
  • Kat2a protein, Xenopus