Comparative analysis of type 2 diabetes-associated SNP alleles identifies allele-specific DNA-binding proteins for the KCNQ1 locus

Hiramoto,Masaki; Udagawa,Haruhide; Watanabe,Atsushi; Miyazawa,Keisuke; Ishibashi,Naoko; Kawaguchi,Miho; Uebanso,Takashi; Nishimura,Wataru; Nammo,Takao; Yasuda,Kazuki

doi:10.3892/ijmm.2015.2203

Comparative analysis of type 2 diabetes-associated SNP alleles identifies allele-specific DNA-binding proteins for the KCNQ1 locus

Authors:
- Masaki Hiramoto
- Haruhide Udagawa
- Atsushi Watanabe
- Keisuke Miyazawa
- Naoko Ishibashi
- Miho Kawaguchi
- Takashi Uebanso
- Wataru Nishimura
- Takao Nammo
- Kazuki Yasuda
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Affiliations: Department of Metabolic Disorder, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, Tokyo 162‑8655, Japan, Laboratory of Research Advancement, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi 474‑8511, Japan, Department of Biochemistry, Tokyo Medical University, Tokyo 160‑8402, Japan
Published online on: May 8, 2015 https://doi.org/10.3892/ijmm.2015.2203
Pages: 222-230

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Abstract

Although recent genome-wide association studies (GWAS) have been extremely successful, it remains a big challenge to functionally annotate disease‑associated single nucleotide polymorphisms (SNPs), as the majority of these SNPs are located in non‑coding regions of the genome. In this study, we described a novel strategy for identifying the proteins that bind to the SNP‑containing locus in an allele‑specific manner and successfully applied this method to SNPs in the type 2 diabetes mellitus susceptibility gene, potassium voltage‑gated channel, KQT‑like subfamily Q, member 1 (KCNQ1). DNA fragments encompassing SNPs, and risk or non‑risk alleles were immobilized onto the novel nanobeads and DNA‑binding proteins were purified from the nuclear extracts of pancreatic β cells using these DNA‑immobilized nanobeads. Comparative analysis of the allele-specific DNA-binding proteins indicated that the affinities of several proteins for the examined SNPs differed between the alleles. Nuclear transcription factor Y (NF‑Y) specifically bound the non‑risk allele of the SNP rs2074196 region and stimulated the transcriptional activity of an artificial promoter containing SNP rs2074196 in an allele‑specific manner. These results suggest that SNP rs2074196 modulates the affinity of the locus for NF‑Y and possibly induces subsequent changes in gene expression. The findings of this study indicate that our comparative method using novel nanobeads is effective for the identification of allele‑specific DNA‑binding proteins, which may provide important clues for the functional impact of disease‑associated non‑coding SNPs.

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1	Imamura M and Maeda S: Genetics of type 2 diabetes: The GWAS era and future perspectives (Review). Endocr J. 58:723–739. 2011. View Article : Google Scholar
2	Yasuda K, Miyake K, Horikawa Y, Hara K, Osawa H, Furuta H, Hirota Y, Mori H, Jonsson A, Sato Y, et al: Variants in KCNQ1 are associated with susceptibility to type 2 diabetes mellitus. Nat Genet. 40:1092–1097. 2008. View Article : Google Scholar : PubMed/NCBI
3	Unoki H, Takahashi A, Kawaguchi T, Hara K, Horikoshi M, Andersen G, Ng DP, Holmkvist J, Borch-Johnsen K, Jørgensen T, et al: SNPs in KCNQ1 are associated with susceptibility to type 2 diabetes in East Asian and European populations. Nat Genet. 40:1098–1102. 2008. View Article : Google Scholar : PubMed/NCBI
4	Voight BF, Scott LJ, Steinthorsdottir V, Morris AP, Dina C, Welch RP, Zeggini E, Huth C, Aulchenko YS, Thorleifsson G, et al: MAGIC investigators; GIANT Consortium: Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nat Genet. 42:579–589. 2010. View Article : Google Scholar : PubMed/NCBI
5	Neyroud N, Tesson F, Denjoy I, Leibovici M, Donger C, Barhanin J, Fauré S, Gary F, Coumel P, Petit C, et al: A novel mutation in the potassium channel gene KVLQT1 causes the Jervell and Lange-Nielsen cardioauditory syndrome. Nat Genet. 15:186–189. 1997. View Article : Google Scholar : PubMed/NCBI
6	Yamagata K, Senokuchi T, Lu M, Takemoto M, Fazlul Karim M, Go C, Sato Y, Hatta M, Yoshizawa T, Araki E, et al: Voltage-gated K⁺ channel KCNQ1 regulates insulin secretion in MIN6 β-cell line. Biochem Biophys Res Commun. 407:620–625. 2011. View Article : Google Scholar : PubMed/NCBI
7	Sanyal A, Lajoie BR, Jain G and Dekker J: The long-range interaction landscape of gene promoters. Nature. 489:109–113. 2012. View Article : Google Scholar : PubMed/NCBI
8	Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, Reynolds AP, Sandstrom R, Qu H, Brody J, et al: Systematic localization of common disease-associated variation in regulatory DNA. Science. 337:1190–1195. 2012. View Article : Google Scholar : PubMed/NCBI
9	Smemo S, Tena JJ, Kim KH, Gamazon ER, Sakabe NJ, Gómez-Marín C, Aneas I, Credidio FL, Sobreira DR, Wasserman NF, et al: Obesity-associated variants within FTO form long-range functional connections with IRX3. Nature. 507:371–375. 2014. View Article : Google Scholar : PubMed/NCBI
10	Pasquali L, Gaulton KJ, Rodríguez-Seguí SA, Mularoni L, Miguel-Escalada I, Akerman I, Tena JJ, Morán I, Gómez-Marín C, van de Bunt M, et al: Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants. Nat Genet. 46:136–143. 2014. View Article : Google Scholar : PubMed/NCBI
11	Kassem SA, Ariel I, Thornton PS, Hussain K, Smith V, Lindley KJ, Aynsley-Green A and Glaser B: p57(KIP2) expression in normal islet cells and in hyperinsulinism of infancy. Diabetes. 50:2763–2769. 2001. View Article : Google Scholar : PubMed/NCBI
12	Avrahami D, Li C, Yu M, Jiao Y, Zhang J, Naji A, Ziaie S, Glaser B and Kaestner KH: Targeting the cell cycle inhibitor p57Kip2 promotes adult human β cell replication. J Clin Invest. 124:670–674. 2014. View Article : Google Scholar : PubMed/NCBI
13	Horike S, Mitsuya K, Meguro M, Kotobuki N, Kashiwagi A, Notsu T, Schulz TC, Shirayoshi Y and Oshimura M: Targeted disruption of the human LIT1 locus defines a putative imprinting control element playing an essential role in Beckwith-Wiedemann syndrome. Hum Mol Genet. 9:2075–2083. 2000. View Article : Google Scholar : PubMed/NCBI
14	Fitzpatrick GV, Soloway PD and Higgins MJ: Regional loss of imprinting and growth deficiency in mice with a targeted deletion of KvDMR1. Nat Genet. 32:426–431. 2002. View Article : Google Scholar : PubMed/NCBI
15	Arima T, Kamikihara T, Hayashida T, Kato K, Inoue T, Shirayoshi Y, Oshimura M, Soejima H, Mukai T and Wake N: ZAC, LIT1 (KCNQ1OT1) and p57KIP2 (CDKN1C) are in an imprinted gene network that may play a role in Beckwith-Wiedemann syndrome. Nucleic Acids Res. 33:2650–2660. 2005. View Article : Google Scholar : PubMed/NCBI
16	Colsoul B, Schraenen A, Lemaire K, Quintens R, Van Lommel L, Segal A, Owsianik G, Talavera K, Voets T, Margolskee RF, et al: Loss of high-frequency glucose-induced Ca²⁺ oscillations in pancreatic islets correlates with impaired glucose tolerance in Trpm5^−/− mice. Proc Natl Acad Sci USA. 107:5208–5213. 2010. View Article : Google Scholar
17	Brixel LR, Monteilh-Zoller MK, Ingenbrandt CS, Fleig A, Penner R, Enklaar T, Zabel BU and Prawitt D: TRPM5 regulates glucose-stimulated insulin secretion. Pflugers Arch. 460:69–76. 2010. View Article : Google Scholar : PubMed/NCBI
18	Kyriazis GA, Soundarapandian MM and Tyrberg B: Sweet taste receptor signaling in beta cells mediates fructose-induced potentiation of glucose-stimulated insulin secretion. Proc Natl Acad Sci USA. 109:E524–E532. 2012. View Article : Google Scholar : PubMed/NCBI
19	Krishnan K, Ma Z, Björklund A and Islam MS: Role of transient receptor potential melastatin-like subtype 5 channel in insulin secretion from rat β-cells. Pancreas. 43:597–604. 2014. View Article : Google Scholar : PubMed/NCBI
20	Kawaguchi H, Asai A, Ohtsuka Y, Watanabe H, Wada T and Handa H: Purification of DNA-binding transcription factors by their selective adsorption on the affinity latex particles. Nucleic Acids Res. 17:6229–6240. 1989. View Article : Google Scholar : PubMed/NCBI
21	Inomata Y, Kawaguchi H, Hiramoto M, Wada T and Handa H: Direct purification of multiple ATF/E4TF3 polypeptides from HeLa cell crude nuclear extracts using DNA affinity latex particles. Anal Biochem. 206:109–114. 1992. View Article : Google Scholar : PubMed/NCBI
22	Wada T, Takagi T, Yamaguchi Y, Kawase H, Hiramoto M, Ferdous A, Takayama M, Lee KA, Hurst HC and Handa H: Copurification of casein kinase II with transcription factor ATF/E4TF3. Nucleic Acids Res. 24:876–884. 1996. View Article : Google Scholar : PubMed/NCBI
23	Nishio K, Masaike Y, Ikeda M, Narimatsu H, Gokon N, Tsubouchi S, Hatakeyama M, Sakamoto S, Hanyu N, Sandhu A, et al: Development of novel magnetic nano-carriers for high-performance affinity purification. Colloids Surf B Biointerfaces. 64:162–169. 2008. View Article : Google Scholar : PubMed/NCBI
24	Asfari M, Janjic D, Meda P, Li G, Halban PA and Wollheim CB: Establishment of 2-mercaptoethanol-dependent differentiated insulin-secreting cell lines. Endocrinology. 130:167–178. 1992.PubMed/NCBI
25	Wada T, Watanabe H, Kawaguchi H and Handa H: DNA affinity chromatography. Methods Enzymol. 254:595–604. 1995. View Article : Google Scholar : PubMed/NCBI
26	Dignam JD, Lebovitz RM and Roeder RG: Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res. 11:1475–1489. 1983. View Article : Google Scholar : PubMed/NCBI
27	Shevchenko A, Wilm M, Vorm O and Mann M: Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal Chem. 68:850–858. 1996. View Article : Google Scholar : PubMed/NCBI
28	Hiramoto M, Maekawa N, Kuge T, Ayabe F, Watanabe A, Masaike Y, Hatakeyama M, Handa H and Imai T: High-performance affinity chromatography method for identification of L-arginine interacting factors using magnetic nanobeads. Biomed Chromatogr. 24:606–612. 2010.
29	Bungartz G, Land H, Scadden DT and Emerson SG: NF-Y is necessary for hematopoietic stem cell proliferation and survival. Blood. 119:1380–1389. 2012. View Article : Google Scholar :
30	Luo R, Klumpp SA, Finegold MJ and Maity SN: Inactivation of CBF/NF-Y in postnatal liver causes hepatocellular degeneration, lipid deposition, and endoplasmic reticulum stress. Sci Rep. 1:1362011. View Article : Google Scholar :