title: The TCF C-clamp DNA binding domain expands the Wnt transcriptome via alternative target recognition.
abstract: 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.
authors.affiliation: Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA 92697, USA.
authors.forename: Nate P
authors.initials: NP
authors.lastname: Hoverter
authors.affiliation: Department of Information and Computer Science, University of California, Irvine, Irvine, CA 92697, USA.
authors.forename: Michael D
authors.initials: MD
authors.lastname: Zeller
authors.affiliation: Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA 92697, USA.
authors.forename: Miriam M
authors.initials: MM
authors.lastname: McQuade
authors.affiliation: Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA 92697, USA.
authors.forename: Angela
authors.initials: A
authors.lastname: Garibaldi
authors.affiliation: Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA 92697, USA.
authors.forename: Anke
authors.initials: A
authors.lastname: Busch
authors.affiliation: Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA 92697, USA.
authors.forename: Elizabeth M
authors.initials: EM
authors.lastname: Selwan
authors.affiliation: Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA 92697, USA.
authors.forename: Klemens J
authors.initials: KJ
authors.lastname: Hertel
authors.affiliation: Department of Information and Computer Science, University of California, Irvine, Irvine, CA 92697, USA.
authors.forename: Pierre
authors.initials: P
authors.lastname: Baldi
authors.affiliation: Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA 92697, USA marian.waterman@uci.edu.
authors.forename: Marian L
authors.initials: ML
authors.lastname: Waterman
mesh_terms: D000818:Animals; D019556:COS Cells; D045744:Cell Line, Tumor; D002522:Chlorocebus aethiops; D047369:Chromatin Immunoprecipitation; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D005786:Gene Expression Regulation; D056426:Genetic Loci; D051538:Hepatocyte Nuclear Factor 1-alpha / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D009154:Mutation; D059372:Nucleotide Motifs; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D020218:Response Elements; D017422:Sequence Analysis, DNA; D013891:Thiouridine; D059467:Transcriptome; D060449:Wnt Signaling Pathway
chemical_list: C496487:HNF1A protein, human; D051538:Hepatocyte Nuclear Factor 1-alpha; D013891:Thiouridine; D004247:DNA