Brahmachary Manisha, Guilmatre Audrey, Quilez Javier, Hasson Dan, Borel Christelle, Warburton Peter, Sharp Andrew J
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.
PLoS Genet. 2014 Jun 19;10(6):e1004418. doi: 10.1371/journal.pgen.1004418. eCollection 2014 Jun.
Tandem repeats are common in eukaryotic genomes, but due to difficulties in assaying them remain poorly studied. Here, we demonstrate the utility of Nanostring technology as a targeted approach to perform accurate measurement of tandem repeats even at extremely high copy number, and apply this technology to genotype 165 HapMap samples from three different populations and five species of non-human primates. We observed extreme variability in copy number of tandemly repeated genes, with many loci showing 5-10 fold variation in copy number among humans. Many of these loci show hallmarks of genome assembly errors, and the true copy number of many large tandem repeats is significantly under-represented even in the high quality 'finished' human reference assembly. Importantly, we demonstrate that most large tandem repeat variations are not tagged by nearby SNPs, and are therefore essentially invisible to SNP-based GWAS approaches. Using association analysis we identify many cis correlations of large tandem repeat variants with nearby gene expression and DNA methylation levels, indicating that variations of tandem repeat length are associated with functional effects on the local genomic environment. This includes an example where expansion of a macrosatellite repeat is associated with increased DNA methylation and suppression of nearby gene expression, suggesting a mechanism termed "repeat induced gene silencing", which has previously been observed only in transgenic organisms. We also observed multiple signatures consistent with altered selective pressures at tandemly repeated loci, suggesting important biological functions. Our studies show that tandemly repeated loci represent a highly variable fraction of the genome that have been systematically ignored by most previous studies, copy number variation of which can exert functionally significant effects. We suggest that future studies of tandem repeat loci will lead to many novel insights into their role in modulating both genomic and phenotypic diversity.
串联重复序列在真核生物基因组中很常见，但由于检测困难，对它们的研究仍然很少。在这里，我们证明了纳米孔技术作为一种靶向方法的实用性，即使在极高拷贝数下也能准确测量串联重复序列，并将该技术应用于对来自三个不同人群和五种非人类灵长类动物的165个HapMap样本进行基因分型。我们观察到串联重复基因的拷贝数存在极大的变异性，许多位点在人类中的拷贝数有5至10倍的差异。其中许多位点显示出基因组组装错误的特征，即使在高质量的“完成”人类参考组装中，许多大型串联重复序列的真实拷贝数也被严重低估。重要的是，我们证明大多数大型串联重复序列变异未被附近的单核苷酸多态性（SNP）标记，因此基于SNP的全基因组关联研究（GWAS）方法基本上无法检测到它们。通过关联分析，我们确定了许多大型串联重复序列变异与附近基因表达和DNA甲基化水平的顺式相关性，表明串联重复长度的变异与对局部基因组环境的功能影响相关。这包括一个例子，其中一个大卫星重复序列的扩增与DNA甲基化增加和附近基因表达的抑制相关，提示了一种称为“重复诱导基因沉默”的机制，该机制以前仅在转基因生物中观察到。我们还观察到多个与串联重复位点选择性压力改变一致的特征，表明其具有重要的生物学功能。我们的研究表明，串联重复位点代表了基因组中一个高度可变的部分，此前大多数研究都系统地忽略了这一部分，其拷贝数变异可产生功能上的显著影响。我们建议，未来对串联重复位点的研究将为它们在调节基因组和表型多样性中的作用带来许多新的见解。
