The TCF C-clamp DNA binding domain expands the Wnt transcriptome via alternative target recognition

• Published in: Nucleic acids research 2014-12, Vol.42 (22), p.13615-13632
• Main Authors: Hoverter, Nate P, Zeller, Michael D, McQuade, Miriam M, Garibaldi, Angela, Busch, Anke, Selwan, Elizabeth M, Hertel, Klemens J, Baldi, Pierre, Waterman, Marian L
• Format: Article
• Language: English
• Subjects: Animals; Cell Line, Tumor; Chlorocebus aethiops; Chromatin Immunoprecipitation; COS Cells; DNA - chemistry; DNA - metabolism; Gene Expression Regulation; Gene regulation, Chromatin and Epigenetics; Genetic Loci; Hepatocyte Nuclear Factor 1-alpha - chemistry; Hepatocyte Nuclear Factor 1-alpha - genetics; Hepatocyte Nuclear Factor 1-alpha - metabolism; Humans; Mutation; Nucleotide Motifs; Protein Binding; Protein Structure, Tertiary; Response Elements; Sequence Analysis, DNA; Thiouridine; Transcriptome; Wnt Signaling Pathway
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gku1186

LEF/TCFs direct the final step in Wnt/β-catenin signalling by recruiting β-catenin to genes for activation of transcription. Ancient, non-vertebrate TCFs contain two DNA binding domains, a High Mobility Group box for recognition of the Wnt Response Element (WRE; 5'-CTTTGWWS-3') and the C-clamp domain for recognition of the GC-rich Helper motif (5'-RCCGCC-3'). Two vertebrate TCFs (TCF-1/TCF7 and TCF-4/TCF7L2) use the C-clamp as an alternatively spliced domain to regulate cell-cycle progression, but how the C-clamp influences TCF binding and activity genome-wide is not known. Here, we used a doxycycline inducible system with ChIP-seq to assess how the C-clamp influences human TCF1 binding genome-wide. Metabolic pulse-labeling of nascent RNA with 4'Thiouridine was used with RNA-seq to connect binding to the Wnt transcriptome. We find that the C-clamp enables targeting to a greater number of gene loci for stronger occupancy and transcription regulation. The C-clamp uses Helper sites concurrently with WREs for gene targeting, but it also targets TCF1 to sites that do not have readily identifiable canonical WREs. The coupled ChIP-seq/4'Thiouridine-seq analysis identified new Wnt target genes, including additional regulators of cell proliferation. Thus, C-clamp containing isoforms of TCFs are potent transcriptional regulators with an expanded transcriptome directed by C-clamp-Helper site interactions.