Linking short tandem repeat polymorphisms with cytosine modifications in human lymphoblastoid cell lines

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• 作者：Zhou Zhang ; Yinan Zheng ; Xu Zhang ; Cong Liu ; Brian Thomas Joyce…
• 刊名：Human Genetics
• 出版年：2016
• 出版时间：February 2016
• 年：2016
• 卷：135
• 期：2
• 页码：223-232
• 全文大小：756 KB
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• 作者单位：Zhou Zhang (1) (2)
  Yinan Zheng (2) (3)
  Xu Zhang (4)
  Cong Liu (5)
  Brian Thomas Joyce (2) (6)
  Warren A. Kibbe (7)
  Lifang Hou (2) (8)
  Wei Zhang (2) (8) (9)
  
  1. Driskill Graduate Program in Life Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
  2. Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Dr., Suite 1400, Chicago, IL, 60611, USA
  3. Institute for Public Health and Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
  4. Section of Hematology/Oncology, Department of Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA
  5. Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, 60612, USA
  6. Division of Epidemiology and Biostatistics, School of Public Health, University of Illinois at Chicago, Chicago, IL, 60612, USA
  7. Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD, 20850, USA
  8. The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
  9. Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
  
• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Biomedicine
  Human Genetics
  Molecular Medicine
  Internal Medicine
  Metabolic Diseases
  
• 出版者：Springer Berlin / Heidelberg
• ISSN：1432-1203

文摘

Inter-individual variation in cytosine modifications has been linked to complex traits in humans. Cytosine modification variation is partially controlled by single nucleotide polymorphisms (SNPs), known as modified cytosine quantitative trait loci (mQTL). However, little is known about the role of short tandem repeat polymorphisms (STRPs), a class of structural genetic variants, in regulating cytosine modifications. Utilizing the published data on the International HapMap Project lymphoblastoid cell lines (LCLs), we assessed the relationships between 721 STRPs and the modification levels of 283,540 autosomal CpG sites. Our findings suggest that, in contrast to the predominant cis-acting mode for SNP-based mQTL, STRPs are associated with cytosine modification levels in both cis-acting (local) and trans-acting (distant) modes. In local scans within the ±1 Mb windows of target CpGs, 21, 9, and 21 cis-acting STRP-based mQTL were detected in CEU (Caucasian residents from Utah, USA), YRI (Yoruba people from Ibadan, Nigeria), and the combined samples, respectively. In contrast, 139,420, 76,817, and 121,866 trans-acting STRP-based mQTL were identified in CEU, YRI, and the combined samples, respectively. A substantial proportion of CpG sites detected with local STRP-based mQTL were not associated with SNP-based mQTL, suggesting that STRPs represent an independent class of mQTL. Functionally, genetic variants neighboring CpG-associated STRPs are enriched with genome-wide association study (GWAS) loci for a variety of complex traits and diseases, including cancers, based on the National Human Genome Research Institute (NHGRI) GWAS Catalog. Therefore, elucidating these STRP-based mQTL in addition to SNP-based mQTL can provide novel insights into the genetic architectures of complex traits. L. Hou and W. Zhang contributed equally to this work as senior authors.Electronic supplementary materialThe online version of this article (doi:10.​1007/​s00439-015-1628-4) contains supplementary material, which is available to authorized users.