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Identification of a functional variant in the KIF5A-CYP27B1-METTL1-FAM119B locus associated with multiple sclerosis.

Abstract

BACKGROUND AND AIM

Several studies have highlighted the association of the 12q13.3-12q14.1 region with coeliac disease, type 1 diabetes, rheumatoid arthritis and multiple sclerosis (MS); however, the causal variants underlying diseases are still unclear. The authors sought to identify the functional variant of this region associated with MS.

METHODS

Tag-single nucleotide polymorphism (SNP) analysis of the associated region encoding 15 genes was performed in 2876 MS patients and 2910 healthy Caucasian controls together with expression regulation analyses.

RESULTS

rs6581155, which tagged 18 variants within a region where 9 genes map, was sufficient to model the association. This SNP was in total linkage disequilibrium (LD) with other polymorphisms that associated with the expression levels of FAM119B, AVIL, TSFM, TSPAN31 and CYP27B1 genes in different expression quantitative trait loci studies. Functional annotations from Encyclopedia of DNA Elements (ENCODE) showed that six out of these rs6581155-tagged-SNPs were located in regions with regulatory potential and only one of them, rs10877013, exhibited allele-dependent (ratio A/G=9.5-fold) and orientation-dependent (forward/reverse=2.7-fold) enhancer activity as determined by luciferase reporter assays. This enhancer is located in a region where a long-range chromatin interaction among the promoters and promoter-enhancer of several genes has been described, possibly affecting their expression simultaneously.

CONCLUSIONS

This study determines a functional variant which alters the enhancer activity of a regulatory element in the locus affecting the expression of several genes and explains the association of the 12q13.3-12q14.1 region with MS.

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  • Authors+Show Affiliations

    ,

    Department of Cell Biology and Immunology Instituto de Parasitología y Biomedicina López Neyra, Consejo Superior de Investigaciones Científicas (IPBLNCSIC), Granada, Spain.

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    Source

    Journal of medical genetics 50:1 2013 Jan pg 25-33

    MeSH

    25-Hydroxyvitamin D3 1-alpha-Hydroxylase
    Chromosome Mapping
    Chromosomes, Human, Pair 12
    Enhancer Elements, Genetic
    Genetic Predisposition to Disease
    Genome-Wide Association Study
    Humans
    Kinesin
    Methyltransferases
    Multiple Sclerosis
    Polymorphism, Single Nucleotide
    Quantitative Trait Loci
    Transcription, Genetic

    Pub Type(s)

    Journal Article
    Research Support, Non-U.S. Gov't

    Language

    eng

    PubMed ID

    23160276

    Citation

    Alcina, Antonio, et al. "Identification of a Functional Variant in the KIF5A-CYP27B1-METTL1-FAM119B Locus Associated With Multiple Sclerosis." Journal of Medical Genetics, vol. 50, no. 1, 2013, pp. 25-33.
    Alcina A, Fedetz M, Fernández O, et al. Identification of a functional variant in the KIF5A-CYP27B1-METTL1-FAM119B locus associated with multiple sclerosis. J Med Genet. 2013;50(1):25-33.
    Alcina, A., Fedetz, M., Fernández, O., Saiz, A., Izquierdo, G., Lucas, M., ... Matesanz, F. (2013). Identification of a functional variant in the KIF5A-CYP27B1-METTL1-FAM119B locus associated with multiple sclerosis. Journal of Medical Genetics, 50(1), pp. 25-33. doi:10.1136/jmedgenet-2012-101085.
    Alcina A, et al. Identification of a Functional Variant in the KIF5A-CYP27B1-METTL1-FAM119B Locus Associated With Multiple Sclerosis. J Med Genet. 2013;50(1):25-33. PubMed PMID: 23160276.
    * Article titles in AMA citation format should be in sentence-case
    TY - JOUR T1 - Identification of a functional variant in the KIF5A-CYP27B1-METTL1-FAM119B locus associated with multiple sclerosis. AU - Alcina,Antonio, AU - Fedetz,Maria, AU - Fernández,Oscar, AU - Saiz,Albert, AU - Izquierdo,Guillermo, AU - Lucas,Miguel, AU - Leyva,Laura, AU - García-León,Juan-Antonio, AU - Abad-Grau,María Del Mar, AU - Alloza,Iraide, AU - Antigüedad,Alfredo, AU - Garcia-Barcina,María J, AU - Vandenbroeck,Koen, AU - Varadé,Jezabel, AU - de la Hera,Belén, AU - Arroyo,Rafael, AU - Comabella,Manuel, AU - Montalban,Xavier, AU - Petit-Marty,Natalia, AU - Navarro,Arcadi, AU - Otaegui,David, AU - Olascoaga,Javier, AU - Blanco,Yolanda, AU - Urcelay,Elena, AU - Matesanz,Fuencisla, Y1 - 2012/11/17/ PY - 2012/11/20/entrez PY - 2012/11/20/pubmed PY - 2013/5/17/medline SP - 25 EP - 33 JF - Journal of medical genetics JO - J. Med. Genet. VL - 50 IS - 1 N2 - BACKGROUND AND AIM: Several studies have highlighted the association of the 12q13.3-12q14.1 region with coeliac disease, type 1 diabetes, rheumatoid arthritis and multiple sclerosis (MS); however, the causal variants underlying diseases are still unclear. The authors sought to identify the functional variant of this region associated with MS. METHODS: Tag-single nucleotide polymorphism (SNP) analysis of the associated region encoding 15 genes was performed in 2876 MS patients and 2910 healthy Caucasian controls together with expression regulation analyses. RESULTS: rs6581155, which tagged 18 variants within a region where 9 genes map, was sufficient to model the association. This SNP was in total linkage disequilibrium (LD) with other polymorphisms that associated with the expression levels of FAM119B, AVIL, TSFM, TSPAN31 and CYP27B1 genes in different expression quantitative trait loci studies. Functional annotations from Encyclopedia of DNA Elements (ENCODE) showed that six out of these rs6581155-tagged-SNPs were located in regions with regulatory potential and only one of them, rs10877013, exhibited allele-dependent (ratio A/G=9.5-fold) and orientation-dependent (forward/reverse=2.7-fold) enhancer activity as determined by luciferase reporter assays. This enhancer is located in a region where a long-range chromatin interaction among the promoters and promoter-enhancer of several genes has been described, possibly affecting their expression simultaneously. CONCLUSIONS: This study determines a functional variant which alters the enhancer activity of a regulatory element in the locus affecting the expression of several genes and explains the association of the 12q13.3-12q14.1 region with MS. SN - 1468-6244 UR - https://www.unboundmedicine.com/medline/citation/23160276/Identification_of_a_functional_variant_in_the_KIF5A_CYP27B1_METTL1_FAM119B_locus_associated_with_multiple_sclerosis_ L2 - http://jmg.bmj.com/cgi/pmidlookup?view=long&pmid=23160276 DB - PRIME DP - Unbound Medicine ER -