TRF3, a TATA-box-binding protein-related factor, is vertebrate-specific and widely expressed

Proc Natl Acad Sci U S A. 2003 Dec 9;100(25):14887-91. doi: 10.1073/pnas.2036440100. Epub 2003 Nov 21.


TATA-box-binding protein (TBP) is a highly conserved RNA polymerase II general transcription factor that binds to the core promoter and initiates assembly of the preinitiation complex. Two proteins with high homology to TBP have been found: TBP-related factor 1 (TRF1), described only in Drosophila melanogaster, and TRF2, which is broadly distributed in metazoans. Here, we report the identification and characterization of an additional TBP-related factor, TRF3. TRF3 is virtually identical to TBP in the C-terminal core domain, including all residues involved in DNA binding and interaction with other general transcription factors. Like other TBP family members, the N-terminal region of TRF3 is divergent. The TRF3 gene is present and expressed in vertebrates, from fish through humans, but absent from the genomes of the urochordate Ciona intestinalis and the lower eukaryotes D. melanogaster and Caenorhabditis elegans. TRF3 is a nuclear protein that is present in all human and mouse tissues and cell lines examined. Despite the highly homologous TBP-like C-terminal core domain, gel filtration analysis indicates that the native molecular weight of TRF3 is substantially less than that of TFIID. Interestingly, after mitosis, reimport of TRF3 into the nucleus occurs subsequent to TBP and other basal transcription factors. In summary, TRF3 is a highly conserved vertebrate-specific TRF whose phylogenetic conservation, expression pattern, and other properties are distinct from those of TBP and all other TRFs.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Caenorhabditis elegans / metabolism
  • Cell Line
  • Cell Nucleus / metabolism
  • Chromatography, Gel
  • Ciona intestinalis / metabolism
  • Computational Biology
  • DNA / chemistry
  • Drosophila melanogaster / metabolism
  • Fluorescent Antibody Technique, Indirect
  • HeLa Cells
  • Humans
  • Mice
  • Mitosis
  • Molecular Sequence Data
  • Nuclear Proteins
  • Phylogeny
  • Protein Biosynthesis
  • Protein Structure, Tertiary
  • RNA Polymerase II / metabolism
  • Reverse Transcriptase Polymerase Chain Reaction
  • Sequence Homology, Amino Acid
  • TATA Box Binding Protein-Like Proteins / chemistry
  • TATA Box Binding Protein-Like Proteins / metabolism*
  • TATA Box Binding Protein-Like Proteins / physiology*
  • Tissue Distribution
  • Transcription Factor TFIID / chemistry
  • Transcription Factors / chemistry
  • Transcription Factors / metabolism*
  • Transcription Factors / physiology*
  • Transcription, Genetic


  • Nuclear Proteins
  • TATA Box Binding Protein-Like Proteins
  • TBPL2 protein, human
  • TRF3 protein, mouse
  • Transcription Factor TFIID
  • Transcription Factors
  • DNA
  • RNA Polymerase II

Associated data

  • GENBANK/AY457923
  • GENBANK/AY457924
  • GENBANK/AY457925
  • GENBANK/BK001774