TdIF1 recognizes a specific DNA sequence through its Helix-Turn-Helix and AT-hook motifs to regulate gene transcription

PLoS One. 2013 Jul 10;8(7):e66710. doi: 10.1371/journal.pone.0066710. Print 2013.

Abstract

TdIF1 was originally identified as a protein that directly binds to DNA polymerase TdT. TdIF1 is also thought to function in transcription regulation, because it binds directly to the transcriptional factor TReP-132, and to histone deacetylases HDAC1 and HDAC2. Here we show that TdIF1 recognizes a specific DNA sequence and regulates gene transcription. By constructing TdIF1 mutants, we identify amino acid residues essential for its interaction with DNA. An in vitro DNA selection assay, SELEX, reveals that TdIF1 preferentially binds to the sequence 5'-GNTGCATG-3' following an AT-tract, through its Helix-Turn-Helix and AT-hook motifs. We show that four repeats of this recognition sequence allow TdIF1 to regulate gene transcription in a plasmid-based luciferase reporter assay. We demonstrate that TdIF1 associates with the RAB20 promoter, and RAB20 gene transcription is reduced in TdIF1-knocked-down cells, suggesting that TdIF1 stimulates RAB20 gene transcription.

MeSH terms

  • AT-Hook Motifs / physiology*
  • Base Sequence
  • Binding Sites / genetics
  • Carrier Proteins / chemistry*
  • Carrier Proteins / physiology*
  • DNA / metabolism*
  • DNA-Binding Proteins
  • Gene Expression Regulation
  • HEK293 Cells
  • Helix-Turn-Helix Motifs / physiology*
  • Humans
  • Molecular Sequence Data
  • Nuclear Proteins / chemistry*
  • Nuclear Proteins / physiology*
  • Protein Binding
  • Substrate Specificity / genetics
  • Transcription Factors
  • Transcription, Genetic / genetics
  • rab GTP-Binding Proteins / genetics*
  • rab GTP-Binding Proteins / metabolism

Substances

  • Carrier Proteins
  • DNA-Binding Proteins
  • DNTTIP1 protein, human
  • Nuclear Proteins
  • Transcription Factors
  • DNA
  • Rab20 protein, human
  • rab GTP-Binding Proteins

Grants and funding

No current external funding sources for this study.