Cooperative action of NC2 and Mot1p to regulate TATA-binding protein function across the genome

Genes Dev. 2008 Sep 1;22(17):2359-69. doi: 10.1101/gad.1682308. Epub 2008 Aug 14.


Promoter recognition by TATA-binding protein (TBP) is an essential step in the initiation of RNA polymerase II (pol II) mediated transcription. Genetic and biochemical studies in yeast have shown that Mot1p and NC2 play important roles in inhibiting TBP activity. To understand how TBP activity is regulated in a genome-wide manner, we profiled the binding of TBP, NC2, Mot1p, TFIID, SAGA, and pol II across the yeast genome using chromatin immunoprecipitation (ChIP)-chip for cells in exponential growth and during reprogramming of transcription. We find that TBP, NC2, and Mot1p colocalize at transcriptionally active pol II core promoters. Relative binding of NC2alpha and Mot1p is higher at TATA promoters, whereas NC2beta has a preference for TATA-less promoters. In line with the ChIP-chip data, we isolated a stable TBP-NC2-Mot1p-DNA complex from chromatin extracts. ATP hydrolysis releases NC2 and DNA from the Mot1p-TBP complex. In vivo experiments indicate that promoter dissociation of TBP and NC2 is highly dynamic, which is dependent on Mot1p function. Based on these results, we propose that NC2 and Mot1p cooperate to dynamically restrict TBP activity on transcribed promoters.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphatases
  • Cell Cycle Proteins / physiology
  • DNA Helicases / physiology*
  • Gene Expression Regulation, Fungal
  • Genome, Fungal*
  • Promoter Regions, Genetic
  • RNA Polymerase II / physiology
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / physiology*
  • Saccharomyces cerevisiae Proteins / physiology*
  • TATA-Binding Protein Associated Factors / physiology*
  • TATA-Box Binding Protein / genetics
  • TATA-Box Binding Protein / physiology*
  • Trans-Activators / physiology


  • Cell Cycle Proteins
  • SAGA complex, S cerevisiae
  • SPT15 protein, S cerevisiae
  • Saccharomyces cerevisiae Proteins
  • TATA-Binding Protein Associated Factors
  • TATA-Box Binding Protein
  • Trans-Activators
  • RNA Polymerase II
  • Adenosine Triphosphatases
  • MOT1 protein, S cerevisiae
  • DNA Helicases