Definition of the transcription factor TdIF1 consensus-binding sequence through genomewide mapping of its binding sites

Kotaro Koiwai (Corresponding Author), Takashi Kubota, Nobuhisa Watanabe, Katsutoshi Hori, Osamu Koiwai, Hisao Masai

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

TdIF1 was originally identified as a protein that directly binds to terminal deoxynucleotidyltransferase, TdT. Through in vitro selection assays (SELEX), we recently showed that TdIF1 recognizes both AT-tract and a specific DNA sequence motif, 5′-TGCATG-3′, and can up-regulate the expression of RAB20 through the latter motif. However, whether TdIF1 binds to these sequences in the cells has not been clear and its other target genes remain to be identified. Here, we determined in vivo TdIF1-binding sequences (TdIF1-invivoBMs) on the human chromosomes through ChIP-seq analyses. The result showed a 160-base pair cassette containing ‘AT-tract~palindrome (inverted repeat)~AT-tract’ as a likely target sequence of TdIF1. Interestingly, the core sequence of the palindrome in the TdIF1-invivoBMs shares significant similarity to the above 5′-TGCATG-3′ motif determined by SELEX in vitro. Furthermore, spacer sequences between AT-tract and the palindrome contain many potential transcription factor binding sites. In luciferase assays, TdIF1 can up-regulate transcription activity of the promoters containing the TdIF1-invivoBM, and this effect is mainly through the palindrome. Clusters of this motif were found in the potential target genes. Gene ontology analysis and RT-qPCR showed the enrichment of some candidate targets of TdIF1 among the genes involved in the regulation of ossification. Potential modes of transcription activation by TdIF1 are discussed.
Original languageEnglish
Pages (from-to)242-254
Number of pages13
JournalGenes to Cells
Volume20
Issue number3
Early online date26 Jan 2015
DOIs
Publication statusPublished - Mar 2015

Fingerprint

Consensus Sequence
Transcription Factors
Binding Sites
Up-Regulation
Inverted Repeat Sequences
Genes
Nucleotide Motifs
Gene Ontology
DNA Nucleotidylexotransferase
Human Chromosomes
Luciferases
Osteogenesis
Base Pairing
Transcriptional Activation
Proteins
In Vitro Techniques

Keywords

  • TdIF1
  • RAB20
  • TdIF1-binding sequences
  • ChIP-seq analysis

Cite this

Definition of the transcription factor TdIF1 consensus-binding sequence through genomewide mapping of its binding sites. / Koiwai, Kotaro (Corresponding Author); Kubota, Takashi; Watanabe, Nobuhisa; Hori, Katsutoshi; Koiwai, Osamu; Masai, Hisao.

In: Genes to Cells, Vol. 20, No. 3, 03.2015, p. 242-254.

Research output: Contribution to journalArticle

Koiwai, Kotaro ; Kubota, Takashi ; Watanabe, Nobuhisa ; Hori, Katsutoshi ; Koiwai, Osamu ; Masai, Hisao. / Definition of the transcription factor TdIF1 consensus-binding sequence through genomewide mapping of its binding sites. In: Genes to Cells. 2015 ; Vol. 20, No. 3. pp. 242-254.
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