Definition of the transcription factor Td IF 1 consensus‐binding sequence through genomewide mapping of its binding sites

Td IF 1 was originally identified as a protein that directly binds to terminal deoxynucleotidyltransferase, TdT. Through in vitro selection assays ( SELEX ), we recently showed that Td IF 1 recognizes both AT ‐tract and a specific DNA sequence motif, 5′‐ TGCATG ‐3′, and can up‐regulate the expression of RAB 20 through the latter motif. However, whether Td IF 1 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 Td IF 1‐binding sequences (Td IF 1‐invivo BM s) on the human chromosomes through Ch IP ‐seq analyses. The result showed a 160‐base pair cassette containing ‘ AT ‐tract~palindrome (inverted repeat)~ AT ‐tract’ as a likely target sequence of Td IF 1. Interestingly, the core sequence of the palindrome in the Td IF 1‐invivo BM s 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, Td IF 1 can up‐regulate transcription activity of the promoters containing the Td IF 1‐invivo BM , 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 Td IF 1 among the genes involved in the regulation of ossification. Potential modes of transcription activation by Td IF 1 are discussed.