Maps of Open Chromatin Guide the Functional Follow-Up of Genome-Wide Association Signals: Application to Hematological Traits

English version České info

Turning genetic discoveries identified in genome-wide association (GWA) studies into biological mechanisms is an important challenge in human genetics. Many GWA signals map outside exons, suggesting that the associated variants may lie within regulatory regions. We applied the formaldehyde-assisted isolation of regulatory elements (FAIRE) method in a megakaryocytic and an erythroblastoid cell line to map active regulatory elements at known loci associated with hematological quantitative traits, coronary artery disease, and myocardial infarction. We showed that the two cell types exhibit distinct patterns of open chromatin and that cell-specific open chromatin can guide the finding of functional variants. We identified an open chromatin region at chromosome 7q22.3 in megakaryocytes but not erythroblasts, which harbors the common non-coding sequence variant rs342293 known to be associated with platelet volume and function. Resequencing of this open chromatin region in 643 individuals provided strong evidence that rs342293 is the only putative causative variant in this region. We demonstrated that the C- and G-alleles differentially bind the transcription factor EVI1 affecting PIK3CG gene expression in platelets and macrophages. A protein–protein interaction network including up- and down-regulated genes in Pik3cg knockout mice indicated that PIK3CG is associated with gene pathways with an established role in platelet membrane biogenesis and thrombus formation. Thus, rs342293 is the functional common variant at this locus; to the best of our knowledge this is the first such variant to be elucidated among the known platelet quantitative trait loci (QTLs). Our data suggested a molecular mechanism by which a non-coding GWA index SNP modulates platelet phenotype.

Vyšlo v časopise: Maps of Open Chromatin Guide the Functional Follow-Up of Genome-Wide Association Signals: Application to Hematological Traits. PLoS Genet 7(6): e32767. doi:10.1371/journal.pgen.1002139
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1002139

Souhrn

Zdroje

1. McCarthyMIAbecasisGRCardonLRGoldsteinDBLittleJ 2008 Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet 9 356 369

2. AltshulerDDalyMJLanderES 2008 Genetic mapping in human disease. Science 322 881 888

3. DonnellyP 2008 Progress and challenges in genome-wide association studies in humans. Nature 456 728 731

4. HindorffLASethupathyPJunkinsHARamosEMMehtaJP 2009 Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA 106 9362 9367

5. DimasASDeutschSStrangerBEMontgomerySBBorelC 2009 Common regulatory variation impacts gene expression in a cell type-dependent manner. Science 325 1246 1250

6. NicaACMontgomerySBDimasASStrangerBEBeazleyC 2010 Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. PLoS Genet 6 e1000895 doi:10.1371/journal.pgen.1000895

7. DennisMYParacchiniSScerriTSProkunina-OlssonLKnightJC 2009 A common variant associated with dyslexia reduces expression of the KIAA0319 gene. PLoS Genet 5 e1000436 doi:10.1371/journal.pgen.1000436

8. PomerantzMMAhmadiyehNJiaLHermanPVerziMP 2009 The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer. Nat Genet 41 882 884

9. TuupanenSTurunenMLehtonenRHallikasOVanharantaS 2009 The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling. Nat Genet 41 885 890

10. JiaLLandanGPomerantzMJaschekRHermanP 2009 Functional enhancers at the gene-poor 8q24 cancer-linked locus. PLoS Genet 5 e1000597 doi:10.1371/journal.pgen.1000597

11. VerlaanDJBerlivetSHunninghakeGMMadoreA-MLarivièreM 2009 Allele-specific chromatin remodeling in the ZPBP2/GSDMB/ORMDL3 locus associated with the risk of asthma and autoimmune disease. Am J Hum Genet 85 377 393

12. MusunuruKStrongAFrank-KamenetskyMLeeNEAhfeldtT 2010 From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus. Nature 466 714 719

13. GaultonKJNammoTPasqualiLSimonJMGiresiPG 2010 A map of open chromatin in human pancreatic islets. Nat Genet 42 255 259

14. GiresiPGKimJMcDaniellRMIyerVRLiebJD 2007 FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res 17 877 885

15. NagyPLPriceDH 2009 Formaldehyde-assisted isolation of regulatory elements. Wiley Interdiscip Rev Syst Biol Med 1 400 406

16. SoranzoNSpectorTDManginoMKühnelBRendonA 2009 A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium. Nat Genet 41 1182 1190

17. The ENCODE Project Consortium 2007 Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447 799 816

18. WatkinsNAGusnantoAde BonoBDeSMiranda-SaavedraD 2009 A HaemAtlas: characterising gene expression in differentiated human blood cells. Blood 113 e1 e9

19. The 1000 Genomes Project Consortium 2010 A map of human genome variation from population-scale sequencing. Nature 467 1061 1073

20. SoranzoNRendonAGiegerCJonesCIWatkinsNA 2009 A novel variant on chromosome 7q22.3 associated with mean platelet volume, counts and function. Blood 113 3831 3837

21. RothGJ 1991 Developing relationships: arterial platelet adhesion, glycoprotein Ib, and leucine-rich glycoproteins. Blood 77 5 19

22. SubramanianATamayoPMoothaVKMukherjeeSEbertBL 2005 Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102 15545 15550

23. MatthewsLGopinathGGillespieMCaudyMCroftD 2009 Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res 37 D619 D622

24. CroftDO'KellyGWuGHawRGillespieM 2011 Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res 39 D691 D697

25. WymannMPZvelebilMLaffargueM 2003 Phosphoinositide 3-kinase signalling–which way to target? Trends Pharmacol Sci 24 366 376

26. RückleTSchwarzMKRommelC 2006 PI3Kγ inhibition: towards an ‘aspirin of the 21st century’? Nat Rev Drug Discov 5 903 918

27. HawkinsPTStephensLR 2007 PI3Kγ is a key regulator of inflammatory responses and cardiovascular homeostasis. Science 318 64 66

28. PasquetJ-MGrossBSGratacapM-PQuekLPasquetS 2000 Thrombopoietin potentiates collagen receptor signaling in platelets through a phosphatidylinositol 3-kinase-dependent pathway. Blood 95 3429 3434

29. ZhaoMSongBPuJWadaTReidB 2006 Electrical signals control wound healing through phosphatidylinositol-3-OH kinase-γ and PTEN. Nature 442 457 460

30. HirschEBoscoOTropelPLaffargueMCalvezR 2001 Resistance to thromboembolism in PI3Kγ-deficient mice. FASEB J 15 2019 2021

31. SchoenwaelderSMOnoASturgeonSChanSMManginP 2007 Identification of a unique co-operative phosphoinositide 3-kinase signaling mechanism regulating integrin αIIbβ3 adhesive function in platelets. J Biol Chem 282 28648 28658

32. JonesCIBraySGarnerSFStephensJde BonoB 2009 A functional genomics approach reveals novel quantitative trait loci associated with platelet signalling pathways. Blood 114 1405 1416

33. JohnsonADYanekLRChenM-HFaradayNLarsonMG 2010 Genome-wide meta-analyses identifies seven loci associated with platelet aggregation in response to agonists. Nat Genet 42 608 613

34. BartholomewCKilbeyAClarkA-MWalkerM 1997 The Evi-1 proto-oncogene encodes a transcriptional repressor activity associated with transformation. Oncogene 14 569 577

35. SakamakiSHirayamaYMatsunagaTKurodaHKusakabeT 1999 Transforming growth factor-β1 (TGF-β1) induces thrombopoietin from bone marrow stromal cells, which stimulates the expression of TGF-β receptor on megakaryocytes and, in turn, renders them susceptible to suppression by TGF-β itself with high specificity. Blood 94 1961 1970

36. KurokawaMMitaniKIrieKMatsuyamaTTakahashiT 1998 The oncoprotein Evi-1 represses TGF-β signalling by inhibiting Smad3. Nature 394 92 96

37. KurokawaMMitaniKImaiYOgawaSYazakiY 1998 The t(3;21) fusion product, AML1/Evi-1, interacts with Smad3 and blocks transforming growth factor-β-mediated growth inhibition of myeloid cells. Blood 92 4003 4012

38. SenyukVSinhaKKLiDRinaldiCRYanamandraS 2007 Repression of RUNX1 activity by EVI1: a new role of EVI1 in leukemogenesis. Cancer Res 67 5658 5666

39. MyersSFreemanCAutonADonnellyPMcVeanG 2008 A common sequence motif associated with recombination hot spots and genome instability in humans. Nat Genet 40 1124 1129

40. WitteDPHarrisREJenskiLJLampkinBC 1986 Megakaryoblastic leukemia in an infant: establishment of a megakaryocytic tumor cell line in athymic nude mice. Cancer 58 238 244

41. FugmanDAWitteDPJonesCLAAronowBJLiebermanMA 1990 In vitro establishment and characterization of a human megakaryoblastic cell line. Blood 75 1252 1261

42. LozzioCBLozzioBB 1975 Human chronic myelogenous leukemia cell-line with positive Philadelphia chromosome. Blood 45 321 334

43. AnderssonLCNilssonKGahmbergCG 1979 K562–a human erythroleukemic cell line. Int J Cancer 23 143 147

44. GiresiPGLiebJD 2009 Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements). Methods 48 233 239

45. LucasIPalakodetiAJiangCYoungDJJiangN 2007 High-throughput mapping of origins of replication in human cells. EMBO Rep 8 770 777

46. LawrenceRDay-WilliamsAGMottRBroxholmeJCardonLR 2009 GLIDERS–a web-based search engine for genome-wide linkage disequilibrium between HapMap SNPs. BMC Bioinformatics 10 1 5

47. CarthariusKFrechKGroteKKlockeBHaltmeierM 2005 MatInspector and beyond: promoter analysis based on transcription factor binding sites. Bioinformatics 21 2933 2942

48. YangT-PBeazleyCMontgomerySBDimasASGutierrez-ArcelusM 2010 Genevar: a database and Java application for the analysis and visualization of SNP-gene associations in eQTL studies. Bioinformatics 26 2474 2476

49. SasakiTIrie-SasakiJJonesRGOliveira-dos-SantosAJStanfordWL 2000 Function of PI3Kγ in thymocyte development, T cell activation, and neutrophil migration. Science 287 1040 1046

50. CarbonSIrelandAMungallCJShuSMarshallB 2009 AmiGO: online access to ontology and annotation data. Bioinformatics 25 288 289

51. ForsbergECDownsKMBresnickEH 2000 Direct interaction of NF-E2 with hypersensitive site 2 of the β-globin locus control region in living cells. Blood 96 334 339

52. TijssenMRCvejicAJoshiAHannahRLFerreiraR 2011 Identification of hematopoietic regulators through genome-wide analysis of simultaneous GATA1, GATA2, RUNX1, FLI1, and SCL binding in megakaryocytes. Dev Cell In press