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

Takashi Kubota, Osamu Koiwai, Katsutoshi Hori, Nobuhisa Watanabe, Kotaro Koiwai

Research output: Contribution to journalArticle

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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.

Original languageEnglish
Article numbere66710
Number of pages10
JournalPloS ONE
Volume8
Issue number7
DOIs
Publication statusPublished - 10 Jul 2013

Fingerprint

AT-Hook Motifs
Hooks
DNA sequences
Transcription
transcription (genetics)
Genes
nucleotide sequences
genes
Assays
Histone Deacetylases
Essential Amino Acids
DNA
DNA-Directed DNA Polymerase
Luciferases
DNA-directed DNA polymerase
assays
luciferase
Plasmids
histones
plasmids

Keywords

  • AT-hook motifs
  • base sequence
  • binding sites
  • carrier proteins
  • DNA
  • gene expression regulation
  • HEK293 cells
  • Helix-Turn-Helix motifs
  • humans
  • molecular sequence data
  • nuclear proteins
  • protein binding
  • substrate specificity
  • transcription, genetic
  • rab GTP-binding proteins

Cite this

TdIF1 recognizes a specific DNA sequence through its Helix-Turn-Helix and AT-hook motifs to regulate gene transcription. / Kubota, Takashi; Koiwai, Osamu; Hori, Katsutoshi; Watanabe, Nobuhisa; Koiwai, Kotaro.

In: PloS ONE, Vol. 8, No. 7, e66710, 10.07.2013.

Research output: Contribution to journalArticle

Kubota, Takashi ; Koiwai, Osamu ; Hori, Katsutoshi ; Watanabe, Nobuhisa ; Koiwai, Kotaro. / TdIF1 recognizes a specific DNA sequence through its Helix-Turn-Helix and AT-hook motifs to regulate gene transcription. In: PloS ONE. 2013 ; Vol. 8, No. 7.
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