title: The mechanisms of genome-wide target gene regulation by TCF7L2 in liver cells.
abstract: In the liver Wnt-signaling contributes to the metabolic fate of hepatocytes, but the precise role of the TCF7L2 in this process is unknown. We employed a temporal RNA-Seq approach to examine gene expression 3-96 h following Tcf7l2 silencing in rat hepatoma cells, and combined this with ChIP-Seq to investigate mechanisms of target gene regulation by TCF7L2. Silencing Tcf7l2 led to a time-dependent appearance of 406 differentially expressed genes (DEGs), including key regulators of cellular growth and differentiation, and amino acid, lipid and glucose metabolism. Direct regulation of 149 DEGs was suggested by strong proximal TCF7L2 binding (peak proximity score > 10) and early mRNA expression changes (≤ 18 h). Indirect gene regulation by TCF7L2 likely occurred via alternate transcription factors, including Hnf4a, Foxo1, Cited2, Myc and Lef1, which were differentially expressed following Tcf7l2 knock-down. Tcf7l2-silencing enhanced the expression and chromatin occupancy of HNF4α, and co-siRNA experiments revealed that HNF4α was required for the regulation of a subset of metabolic genes by TCF7L2, particularly those involved in lipid and amino-acid metabolism. Our findings suggest TCF7L2 is an important regulator of the hepatic phenotype, and highlight novel mechanisms of gene regulation by TCF7L2 that involve interplay between multiple hepatic transcriptional pathways.
authors.affiliation: Diabetes Division, University of Texas Health Science Center, San Antonio, TX 78229, USA nortonl@uthscsa.edu.
authors.forename: Luke
authors.initials: L
authors.lastname: Norton
authors.affiliation: Diabetes Division, University of Texas Health Science Center, San Antonio, TX 78229, USA.
authors.forename: Xi
authors.initials: X
authors.lastname: Chen
authors.affiliation: Diabetes Division, University of Texas Health Science Center, San Antonio, TX 78229, USA.
authors.forename: Marcel
authors.initials: M
authors.lastname: Fourcaudot
authors.affiliation: Diabetes Division, University of Texas Health Science Center, San Antonio, TX 78229, USA.
authors.forename: Nikhil K
authors.initials: NK
authors.lastname: Acharya
authors.affiliation: Diabetes Division, University of Texas Health Science Center, San Antonio, TX 78229, USA.
authors.forename: Ralph A
authors.initials: RA
authors.lastname: DeFronzo
authors.affiliation: Institute of Biomedicine, University of Eastern Finland, Kuopio 70211, Finland nortonl@uthscsa.edu.
authors.forename: Sami
authors.identifier: http://orcid.org/0000-0002-6083-2402
authors.initials: S
authors.lastname: Heikkinen
mesh_terms: D000818:Animals; D001665:Binding Sites; D006528:Carcinoma, Hepatocellular / Q000235:genetics / Q000378:metabolism; D045744:Cell Line, Tumor; D047369:Chromatin Immunoprecipitation; D015972:Gene Expression Regulation, Neoplastic; D020868:Gene Silencing; D016678:Genome; D051557:Hepatocyte Nuclear Factor 4 / Q000378:metabolism; D006801:Humans; D008113:Liver Neoplasms / Q000235:genetics / Q000378:metabolism; D008114:Liver Neoplasms, Experimental / Q000235:genetics* / Q000378:metabolism; D051381:Rats; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA; D058118:Transcription Factor 7-Like 2 Protein / Q000235:genetics / Q000378:metabolism*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D051557:Hepatocyte Nuclear Factor 4; D058118:Transcription Factor 7-Like 2 Protein; D014157:Transcription Factors