Cited by 297Genomics and Chromatin DynamicsGenetic Associations and EpidemiologyAsthma and respiratory diseases

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Allele-Specific Chromatin Remodeling in the ZPBP2/GSDMB/ORMDL3 Locus Associated with the Risk of Asthma and Autoimmune Disease

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Verlaan, Dominique J., Berlivet, Soizik, Hunninghake, Gary M., Madore, Anne-Marie, Larivière, Mathieu, Moussette, Sanny, Grundberg, Elin, Kwan, Tony, Ouimet, Manon, Ge, Bing, Hoberman, Rose, Swiatek, Marcin, Dias, Joana, Lam, Kevin C.L., Koka, Vonda, Harmsen, Eef, Soto-Quiros, Manuel, Avila, Lydiana, Celedón, Juan C., Weiss, Scott T., Dewar, Ken, Sinnett, Daniel, Laprise, Catherine, Raby, Benjamin A., Pastinen, Tomi, Naumova, Anna K.·2009·The American Journal of Human Genetics

DOI 10.1016/j.ajhg.2009.08.007PMC PMC2771592

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Abstract

Common SNPs in the chromosome 17q12-q21 region alter the risk for asthma, type 1 diabetes, primary biliary cirrhosis, and Crohn disease. Previous reports by us and others have linked the disease-associated genetic variants with changes in expression of GSDMB and ORMDL3 transcripts in human lymphoblastoid cell lines (LCLs). The variants also alter regulation of other transcripts, and this domain-wide cis-regulatory effect suggests a mechanism involving long-range chromatin interactions. Here, we further dissect the disease-linked haplotype and identify putative causal DNA variants via a combination of genetic and functional analyses. First, high-throughput resequencing of the region and genotyping of potential candidate variants were performed. Next, additional mapping of allelic expression differences in Yoruba HapMap LCLs allowed us to fine-map the basis of the cis-regulatory differences to a handful of candidate functional variants. Functional assays identified allele-specific differences in nucleosome distribution, an allele-specific association with the insulator protein CTCF, as well as a weak promoter activity for rs12936231. Overall, this study shows a common disease allele linked to changes in CTCF binding and nucleosome occupancy leading to altered domain-wide cis-regulation. Finally, a strong association between asthma and cis-regulatory haplotypes was observed in three independent family-based cohorts (p = 1.78 x 10(-8)). This study demonstrates the requirement of multiple parallel allele-specific tools for the investigation of noncoding disease variants and functional fine-mapping of human disease-associated haplotypes.

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Authors: Verlaan, D. J., Berlivet, S., Hunninghake, G. M., Madore, A.-M., Larivière, M., Moussette, S., Grundberg, E., Kwan, T., Ouimet, M., Ge, B., Hoberman, R., Swiatek, M., Dias, J., Lam, K. C. L., Koka, V., Harmsen, E., Soto-Quiros, M., Avila, L., Celedón, J. C., Weiss, S. T., Dewar, K., Sinnett, D., Laprise, C., Raby, B. A., Pastinen, T., & Naumova, A. K.
Affiliations: Centre Hospitalier Universitaire Sainte-Justine (CA)
McGill University (CA)
Brigham and Women's Hospital (US)
Université du Québec à Chicoutimi (CA)
McGill University and Génome Québec Innovation Centre (CA)
Research Institute of the McGill University Health Centre (CA)
Corresponding author: Pastinen, Tomi
ORCID: Hunninghake, Gary M.
Madore, Anne-Marie
Grundberg, Elin
Kwan, Tony
Ouimet, Manon
Ge, Bing
Weiss, Scott T.
Dewar, Ken
Sinnett, Daniel
Laprise, Catherine
Raby, Benjamin A.
Pastinen, Tomi
Naumova, Anna K.
Venue: The American Journal of Human Genetics
Publisher: Elsevier BV
Published: 2009-09
Volume: 85
Issue: 3
Pages: 377-393
ISSN: 0002-9297 (ISSN-L)
DOI: 10.1016/j.ajhg.2009.08.007
PMC: PMC2771592
OpenAlex: W2041155293
Cited by: 297
References: 70
Citations by year: 2026: 2 · 2025: 11 · 2024: 13 · 2023: 18 · 2022: 14 · 2021: 16 · 2020: 16 · 2019: 13 · 2018: 17 · 2017: 18 · 2016: 18 · 2015: 32 · 2014: 17 · 2013: 18 · 2012: 28
FWCI: 9.94
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 1417 d)
Locations: The American Journal of Human Genetics (publishedVersion)
Europe PMC (PubMed Central) (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Funders: National Institutes of Health
National Heart, Lung, and Blood Institute (HL04370, HL66289, T32 HL07427, U01HL065899, R01HL066289, K08HL092222, R37HL066289, K01HL004370, U01HL075419, R01HL086601, P01HL083069, U01 HL65899, T32HL007427)
National Human Genome Research Institute
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
Health Sciences › Medicine › Pulmonary and Respiratory Medicine › Asthma and respiratory diseases
Keywords: asthma, autoimmune disease, type 1 diabetes, primary biliary cirrhosis, Crohn's disease, cis-regulatory variation, long-range chromatin interactions, allele-specific expression, nucleosome occupancy, CTCF binding, insulator proteins
MeSH terms: Gasdermins, Adolescent, Alleles, Asthma, Autoimmune Diseases, Base Sequence, Cell Line, Child, Chromosomes, Human, Pair 17, DNA Mutational Analysis, Egg Proteins, Female, Haplotypes, Humans, Male, Membrane Proteins, Molecular Sequence Data, Neoplasm Proteins, Pedigree, Regulatory Sequences, Nucleic Acid, Genes, Reporter, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Chromatin Assembly and Disassembly, White People

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Allele-Specific Chromatin Remodeling in the ZPBP2/GSDMB/ORMDL3 Locus Associated with the Risk of Asthma and Autoimmune Disease

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