Genome-wide analyses of ChIP-seq derived FOXA2 DNA occupancy in liver points to genetic networks underpinning multiple complex traits

Journal of Clinical Endocrinology and Metabolism

Volumn 99, Issue 8, 2014, Pages

  Johnson, Matthew E ^a   Schug, Jonathan ^b   Wells, Andrew D ^a   Kaestner, Klaus H ^b   Grant, Struan F A ^a,b  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITES; CARDIOVASCULAR DISEASES; CHROMATIN IMMUNOPRECIPITATION; DNA; ENDOCRINE SYSTEM DISEASES; GENE REGULATORY NETWORKS; GENOME-WIDE ASSOCIATION STUDY; HEPATOCYTE NUCLEAR FACTOR 3-BETA; HUMANS; LIVER; MENTAL DISORDERS; METABOLIC NETWORKS AND PATHWAYS; NEOPLASMS; NERVOUS SYSTEM DISEASES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEIN BINDING; QUANTITATIVE TRAIT LOCI;

EID: 84905860812     PISSN: 0021972X     EISSN: 19457197     Source Type: Journal    
DOI: 10.1210/jc.2013-4503     Document Type: Article

References (20)

1. Kaestner KH, Knochel W, Martinez DE. Unified nomenclature for the winged helix/forkhead transcription factors. Genes Dev. 2000; 14:142-146.
2. Kaestner KH. The FoxA factors in organogenesis and differentiation. Curr Opin Genet Dev. 2010;20:527-532.
3. Manning AK, Hivert MF, Scott RA, et al. A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance. Nat Genet. 2012; 44:659-669.
4. Grant SF, Thorleifsson G, Reynisdottir I, et al. Variant of transcription factor 7-like 2 (TCF7L2) gene confers risk of type 2 diabetes. Nat Genet. 2006;38:320-323.
5. Zhao J, Schug J, Li M, Kaestner KH, Grant SF. Disease-associated loci are significantly over-represented among genes bound by transcription factor 7-like 2 (TCF7L2) in vivo. Diabetologia. 2010;53: 2340-2346.
6. Deliard S, Zhao J, Xia Q, Grant SFA. Generation of high quality chromatin immunoprecipitation DNA template for high-throughput sequencing (ChIP-seq). J Vis Exp. 2013;e50286.
7. Soccio RE, Tuteja G, Everett LJ, Li Z, Lazar MA, Kaestner KH. Species-specific strategies underlying conserved functions of metabolic transcription factors. Mol Endocrinol. 2011;25:694-706.
8. Heinz S, Benner C, Spann N, et al. Simple combinations of lineagedetermining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010;38:576-589.
9. Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genomewide expression profiles. Proc Natl Acad Sci USA. 2005;102: 15545-15550.
10. Mootha VK, Lindgren CM, Eriksson KF, et al. PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet. 2003;34:267-273.
11. Kyrmizi I, Hatzis P, Katrakili N, Tronche F, Gonzalez FJ, Talianidis I. Plasticity and expanding complexity of the hepatic transcription factor network during liver development. Genes Dev. 2006;20: 2293-2305.
12. Chen G, Wan H, Luo F, et al. Foxa2 programs Th2 cell-mediated innate immunity in the developing lung. J Immunol. 2010;184: 6133-6141.
13. Liu M, Lee DF, Chen CT, et al. IKK+ activation of NOTCH links tumorigenesis via FOXA2 suppression. Mol Cell. 2012;45:171-184.
14. Pasquali L, Gaulton KJ, Rodriguez-Segui SA, et al. Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants. Nat Genet. 2014;46:136-143.
15. Maurano MT, Humbert R, Rynes E, et al. Systematic localization of common disease-associated variation in regulatory DNA. Science. 2012;337:1190-1195.
16. Ramagopalan SV, Heger A, Berlanga AJ, et al. A ChIP-seq defined genome-wide map of vitamin D receptor binding: associations with disease and evolution. Genome Res. 2010;20:1352-1360.
17. Consortium EP, Dunham I, Kundaje A, et al. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012; 489:57-74.
18. Kaestner KH, Katz J, Liu Y, Drucker DJ, Schutz G. Inactivation of the winged helix transcription factor HNF3- affects glucose homeostasis and islet glucagon gene expression in vivo. Genes Dev. 1999;13:495-504.
19. Pani L, Quian XB, Clevidence D, CostaRH.The restricted promoter activity of the liver transcription factor hepatocyte nuclear factor 3- involves a cell-specific factor and positive autoactivation. Mol Cell Biol. 1992;12:552-562.
20. Yuan X, Waterworth D, Perry JR, et al. Population-based genomewide association studies reveal six loci influencing plasma levels of liver enzymes. Am J Hum Genet. 2008;83:520-528.