SNP-specific array-based allele-specific expression analysis
SNP-specific array-based allele-specific expression analysis
复制标题
DOI：
10.1101/gr.073254.107
复制
发表时间：
2008-05-01
期刊：
影响因子：
7
通讯作者：
Feinberg, Andrew P.
中科院分区：
文献类型：
--
作者：
Bjornsson, Hans T.;Albert, Thomas J.;Feinberg, Andrew P.
我们开发了一种优化的基于阵列的方法，用于可定制的等位基因特异性基因表达（ASE）分析。该方法的核心特征是能够随意选择SNP进行检测，并且不需要PCR扩增靶标。等位基因区分需要令人惊讶的长探针长度（39-49 nt）。复溶实验证明ASE在宽范围内呈线性。使用这种方法，我们已经发现了至少两个新的印记基因，NLRP 2，它编码的炎性小体的成员，和OSBPL 1A，它编码一个假定的氧固醇结合蛋白，都优先从母体等位基因表达。与此相反，ERAP 2，它编码的氨肽酶，没有显示出优先的父母的起源表达，而是顺式作用的非印迹差异等位基因控制。该方法可扩展到整个基因组，并可用于发现患者样品中的功能性表观遗传修饰。
We have developed an optimized array-based approach for customizable allele-specific gene expression (ASE) analysis. The central features of the approach are the ability to select SNPs at will for detection, and the absence of need to PCR amplify the target. A surprisingly long probe length (39-49 nt) was needed for allelic discrimination. Reconstitution experiments demonstrate linearity of ASE over a broad range. Using this approach, we have discovered at least two novel imprinted genes, NLRP2, which encodes a member of the inflammasome, and OSBPL1A, which encodes a presumed oxysterol-binding protein, were both preferentially expressed from the maternal allele. In contrast, ERAP2, which encodes an aminopeptidase, did not show preferential parent-of-origin expression, but rather, cis-acting nonimprinted differential allelic control. The approach is scalable to the whole genome and can be used for discovery of functional epigenetic modifications in patient samples.