Allele-specific transcriptional activity at type 2 diabetes-associated single nucleotide polymorphisms in regions of pancreatic islet open chromatin at the JAZF1 locus

Diabetes

Volumn 62, Issue 5, 2013, Pages 1756-1762

  Fogarty, Marie P ^a   Panhuis, Tami M ^b   Vadlamudi, Swarooparani ^a   Buchkovich, Martin L ^a   Mohlke, Karen L ^a  

^a UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^b OHIO WESLEYAN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MEMBRANE PROTEIN; PROTEIN JAZF1; TRANSCRIPTION FACTOR PDX 1; UNCLASSIFIED DRUG;

ANIMAL CELL; ARTICLE; BINDING AFFINITY; CHROMATIN; CONTROLLED STUDY; FOLLOW UP; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE MAPPING; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; HISTONE MODIFICATION; INSULINOMA; INTRON; NON INSULIN DEPENDENT DIABETES MELLITUS; NONHUMAN; PANCREAS ISLET CELL; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN FUNCTION; RAT; SINGLE NUCLEOTIDE POLYMORPHISM;

ALLELES; ANIMALS; CELL LINE; CHROMATIN; DIABETES MELLITUS, TYPE 2; DNA-BINDING PROTEINS; GENES, REPORTER; GENETIC ASSOCIATION STUDIES; HOMEODOMAIN PROTEINS; HUMANS; INTRONS; ISLETS OF LANGERHANS; LINKAGE DISEQUILIBRIUM; MICE; NEOPLASM PROTEINS; POLYMORPHISM, SINGLE NUCLEOTIDE; RATS; RECOMBINANT PROTEINS; TRANS-ACTIVATORS; TRANSCRIPTION, GENETIC; UTAH;

EID: 84876542426     PISSN: 00121797     EISSN: 1939327X     Source Type: Journal    
DOI: 10.2337/db12-0972     Document Type: Article

References (38)

1. Visscher PM, Brown MA, McCarthy MI, Yang J. Five years of GWAS discovery. Am J Hum Genet 2012;90:7-24
2. Wu C, Wong YC, Elgin SC. The chromatin structure of specific genes: II. Disruption of chromatin structure during gene activity. Cell 1979;16:807-814 (Pubitemid 9161331)
3. Giresi PG, Kim J, McDaniell RM, Iyer VR, Lieb JD. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res 2007;17:877-885 (Pubitemid 46919722)
4. Consortium EP; ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 2004;306:636-640
5. Zhou X, Maricque B, Xie M, et al. The Human Epigenome Browser at Washington University. Nat Methods 2011;8:989-990
6. Stitzel ML, Sethupathy P, Pearson DS, et al.; NISC Comparative Sequencing Program. Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci. Cell Metab 2010;12:443-455
7. Paul DS, Nisbet JP, Yang TP, et al.; Cardiogenics Consortium; MuTHER Consortium. Maps of open chromatin guide the functional follow-up of genome-wide association signals: application to hematological traits. PLoS Genet 2011;7:e1002139
8. Gaulton KJ, Nammo T, Pasquali L, et al. A map of open chromatin in human pancreatic islets. Nat Genet 2010;42:255-259
9. Zeggini E, Scott LJ, Saxena R, et al.; Wellcome Trust Case Control Consortium. Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. Nat Genet 2008;40:638-645 (Pubitemid 351601209)
10. Nakajima T, Fujino S, Nakanishi G, Kim YS, Jetten AM. TIP27: a novel repressor of the nuclear orphan receptor TAK1/TR4. Nucleic Acids Res 2004;32:4194-4204 (Pubitemid 39232292)
11. O'Geen H, Lin YH, Xu X, et al. Genome-wide binding of the orphan nuclear receptor TR4 suggests its general role in fundamental biological processes. BMC Genomics 2010;11:689
12. Collins LL, Lee YF, Heinlein CA, et al. Growth retardation and abnormal maternal behavior in mice lacking testicular orphan nuclear receptor 4. Proc Natl Acad Sci USA 2004;101:15058-15063 (Pubitemid 39391718)
13. Kang HS, Okamoto K, Kim YS, et al. Nuclear orphan receptor TAK1/TR4-deficient mice are protected against obesity-linked inflammation, hepatic steatosis, and insulin resistance. Diabetes 2011;60:177-188
14. Grarup N, Andersen G, Krarup NT, et al. Association testing of novel type 2 diabetes risk alleles in the JAZF1, CDC123/CAMK1D, TSPAN8, THADA, ADAMTS9, and NOTCH2 loci with insulin release, insulin sensitivity, and obesity in a population-based sample of 4,516 glucose-tolerant middle-aged Danes. Diabetes 2008;57:2534-2540
15. Taneera J, Lang S, Sharma A, et al. A systems genetics approach identifies genes and pathways for type 2 diabetes in human islets. Cell Metab 2012;16:122-134
16. Johansson A, Marroni F, Hayward C, et al.; EUROSPAN Consortium. Common variants in the JAZF1 gene associated with height identified by linkage and genome-wide association analysis. Hum Mol Genet 2009;18:373-380
17. Thomas G, Jacobs KB, Yeager M, et al. Multiple loci identified in a genome-wide association study of prostate cancer. Nat Genet 2008;40:310-315 (Pubitemid 351311773)
18. Voight BF, Scott LJ, Steinthorsdottir V, et al.; MAGIC investigators; GIANT Consortium. Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nat Genet 2010;42:579-589
19. Zhong H, Yang X, Kaplan LM, Molony C, Schadt EE. Integrating pathway analysis and genetics of gene expression for genome-wide association studies. Am J Hum Genet 2010;86:581-591
20. Sharma NK, Langberg KA, Mondal AK, Elbein SC, Das SK. Type 2 diabetes (T2D) associated polymorphisms regulate expression of adjacent transcripts in transformed lymphocytes, adipose, and muscle from Caucasian and African-American subjects. J Clin Endocrinol Metab 2011;96:E394-E403
21. Hohmeier HE, Mulder H, Chen G, Henkel-Rieger R, Prentki M, Newgard CB. Isolation of INS-1-derived cell lines with robust ATP-sensitive K+ channel-dependent and -independent glucose-stimulated insulin secretion. Diabetes 2000;49:424-430 (Pubitemid 30131788)
22. Miyazaki J, Araki K, Yamato E, et al. Establishment of a pancreatic beta cell line that retains glucose-inducible insulin secretion: special reference to expression of glucose transporter isoforms. Endocrinology 1990;127:126-132 (Pubitemid 20228111)
23. Song L, Zhang Z, Grasfeder LL, et al. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res 2011;21:1757-1767
24. Creyghton MP, Cheng AW, Welstead GG, et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci USA 2010;107:21931-21936
25. Heintzman ND, Hon GC, Hawkins RD, et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 2009;459:108-112
26. Bryne JC, Valen E, Tang MH, et al. JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. Nucleic Acids Res 2008;36(Database issue):D102-D106 (Pubitemid 351149704)
27. Saxena R, Elbers CC, Guo Y, et al.; Look AHEAD Research Group; DIAGRAM consortium. Large-scale gene-centric meta-analysis across 39 studies identifies type 2 diabetes loci. Am J Hum Genet 2012;90:410-425
28. Morris AP, Voight BF, Teslovich TM, et al.; Wellcome Trust Case Control Consortium; Meta-Analyses of Glucose and Insulin-related traits Consortium (MAGIC) Investigators; Genetic Investigation of ANthropometric Traits (GIANT) Consortium; Asian Genetic Epidemiology Network-Type 2 Diabetes (AGEN-T2D) Consortium; South Asian Type 2 Diabetes (SAT2D) Consortium; DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium. Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes. Nat Genet 2012;44:981-990
29. Visel A, Blow MJ, Li Z, et al. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 2009;457:854-858
30. Stratigopoulos G, LeDuc CA, Cremona ML, Chung WK, Leibel RL. Cut-like homeobox 1 (CUX1) regulates expression of the fat mass and obesity-associated and retinitis pigmentosa GTPase regulator-interacting protein-1-like (RPGRIP1L) genes and coordinates leptin receptor signaling. J Biol Chem 2011;286:2155-2170
31. Macfarlane WM, Frayling TM, Ellard S, et al. Missense mutations in the insulin promoter factor-1 gene predispose to type 2 diabetes. J Clin Invest 1999;104:R33-R39 (Pubitemid 29536302)
32. Hani EH, Stoffers DA, Chèvre JC, et al. Defective mutations in the insulin promoter factor-1 (IPF-1) gene in late-onset type 2 diabetes mellitus. J Clin Invest 1999;104:R41-R48 (Pubitemid 29536303)
33. Stoffers DA, Ferrer J, Clarke WL, Habener JF. Early-onset type-II diabetes mellitus (MODY4) linked to IPF1. Nat Genet 1997;17:138-139
34. Waeber G, Thompson N, Nicod P, Bonny C. Transcriptional activation of the GLUT2 gene by the IPF-1/STF-1/IDX-1 homeobox factor. Mol Endocrinol 1996;10:1327-1334 (Pubitemid 26423223)
35. Petersen HV, Serup P, Leonard J, Michelsen BK, Madsen OD. Transcriptional regulation of the human insulin gene is dependent on the homeodomain protein STF1/IPF1 acting through the CT boxes. Proc Natl Acad Sci USA 1994;91:10465-10469 (Pubitemid 24329018)
36. Khoo C, Yang J, Weinrott SA, et al. Research resource: the pdx1 cistrome of pancreatic islets. Mol Endocrinol 2012;26:521-533
37. Eizirik DL, Sammeth M, Bouckenooghe T, et al. The human pancreatic islet transcriptome: expression of candidate genes for type 1 diabetes and the impact of pro-inflammatory cytokines. PLoS Genet 2012;8:e1002552
38. Fujita PA, Rhead B, Zweig AS, et al. The UCSC Genome Browser database: update 2011. Nucleic Acids Res 2011;39(Database issue):D876-D882