| Title |
Linking short tandem repeat polymorphisms with cytosine modifications in human lymphoblastoid cell lines
|
|---|---|
| Published in |
Human Genetics, December 2015
|
| DOI | 10.1007/s00439-015-1628-4 |
| Pubmed ID | |
| Authors |
Zhou Zhang, Yinan Zheng, Xu Zhang, Cong Liu, Brian Thomas Joyce, Warren A. Kibbe, Lifang Hou, Wei Zhang |
| Abstract |
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. |
X Demographics
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Geographical breakdown
| Country | Count | As % |
|---|---|---|
| France | 1 | 50% |
| United Kingdom | 1 | 50% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 1 | 50% |
| Scientists | 1 | 50% |
Mendeley readers
The data shown below were compiled from readership statistics for 13 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Germany | 1 | 8% |
| Unknown | 12 | 92% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 3 | 23% |
| Researcher | 3 | 23% |
| Student > Bachelor | 2 | 15% |
| Professor | 1 | 8% |
| Other | 1 | 8% |
| Other | 1 | 8% |
| Unknown | 2 | 15% |
| Readers by discipline | Count | As % |
|---|---|---|
| Biochemistry, Genetics and Molecular Biology | 5 | 38% |
| Engineering | 2 | 15% |
| Agricultural and Biological Sciences | 1 | 8% |
| Chemistry | 1 | 8% |
| Computer Science | 1 | 8% |
| Other | 0 | 0% |
| Unknown | 3 | 23% |
Attention Score in Context
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#15,352,477
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Outputs from Human Genetics
#2,540
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Outputs of similar age
#230,601
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Outputs of similar age from Human Genetics
#15
of 24 outputs
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