Definition of the transcription factor TdIF1 consensus‐binding sequence through genomewide mapping of its binding sites. (26th January 2015)

• Record Type: Journal Article
• Authors: Koiwai, Kotaro; Kubota, Takashi; Watanabe, Nobuhisa; Hori, Katsutoshi; Koiwai, Osamu; Masai, Hisao
• Is Part Of: Genes to cells. Volume 20:Number 3(2015:Mar.)
• Page Start: 242
• Page End: 254
• Publication Date: 2015-01-26
• Subjects: Cytogenetics -- Periodicals; Cells -- Mechanical properties -- Periodicals; Molecular genetics -- Periodicals; Genes -- Periodicals; Molecular biology -- Periodicals; Cytology -- Periodicals; Biomechanics -- Periodicals; 571.6
• DOI: 10.1111/gtc.12216
• Languages: English
• ISSNs: 1356-9597

Abstract

<abstract abstract-type="main" id="gtc12216-abs-0001"> <title> <x xml:space="preserve">Abstract</x> </title> <p>TdIF1 was originally identified as a protein that directly binds to terminal deoxynucleotidyltransferase, TdT. Through <italic>in vitro</italic> 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 <italic>RAB20</italic> 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 <italic>in vivo</italic> 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 <italic>in vitro</italic>. 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.</p> </abstract>