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Linking short tandem repeat polymorphisms with cytosine modifications in human lymphoblastoid cell lines
Zhou Zhang1,2, Yinan Zheng2,3, Xu Zhang4
1Driskill Graduate Program in Life Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
Human Genetics
|December 31, 2015
Summary
Short tandem repeat polymorphisms (STRPs) regulate cytosine modifications through local and distant effects, independent of single nucleotide polymorphisms (SNPs). These STRPs offer new insights into complex traits and diseases.
Area of Science:
- Genetics
- Epigenetics
- Genomics
Background:
- Inter-individual variation in cytosine modifications is linked to complex human traits.
- Single nucleotide polymorphisms (SNPs) are known regulators of cytosine modification variation (mQTL).
- The role of short tandem repeat polymorphisms (STRPs) in regulating cytosine modifications remains largely unexplored.
Purpose of the Study:
- To investigate the association between STRPs and cytosine modification levels.
- To determine if STRPs act in cis or trans to influence cytosine modifications.
- To compare STRP-based mQTL with SNP-based mQTL and explore their functional implications.
Main Methods:
- Utilized published data from the International HapMap Project lymphoblastoid cell lines (LCLs).
- Assessed relationships between 721 STRPs and 283,540 autosomal CpG sites.
- Performed local (±1 Mb) and trans scans to identify STRP-based mQTL in different populations (CEU, YRI) and combined samples.
Main Results:
- STRPs were found to associate with cytosine modification levels in both cis and trans modes.
- Detected 21, 9, and 21 cis-acting STRP-based mQTL in CEU, YRI, and combined samples, respectively.
- Identified a substantial number of trans-acting STRP-based mQTL (139,420 in CEU, 76,817 in YRI, 121,866 combined).
- A significant proportion of cis-acting STRP-mQTL were not linked to SNP-mQTL, indicating STRPs as a distinct mQTL class.
- Genetic variants near CpG-associated STRPs are enriched with GWAS loci for complex traits and diseases, including cancers.
Conclusions:
- STRPs represent a novel class of modified cytosine quantitative trait loci (mQTL) acting in both cis and trans.
- STRP-based mQTL provide a new avenue for understanding the genetic architecture of complex traits and diseases.
- Elucidating STRP-based mQTL alongside SNP-based mQTL is crucial for a comprehensive view of genetic regulation of epigenetics.
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