Critical evaluation of imprinted gene expression by RNA-Seq: a new perspective.
Critical evaluation of imprinted gene expression by RNA-Seq: a new perspective.
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通过RNA-Seq对印迹基因表达的批判性评估：一种新的观点。
DOI：
10.1371/journal.pgen.1002600
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发表时间：
2012
期刊：
影响因子：
4.5
通讯作者：
Babak T
中科院分区：
文献类型：
--
作者：
DeVeale B;van der Kooy D;Babak T
与现有的大约200个鼠印在基因的估计值相反，最近的工作基于转录组测序，在发育中的大脑和两个成年大脑区域中，在1,300多个局部局部的原始父母等位基因效应，包括男性或女性中的数百个。我们对胚胎脑阶段的独立复制，在该阶段中发现了大多数新型印迹基因，并且大多数先前已知的印迹基因证实，都导致了在新型的基因座中，只有12.9％的一致性。 （ASE）用RNA – Seq测得的（ASE）未通过统计方法进行准确建模，这些方法假设随机独立采样，并且必须考虑系统误差为了准确地识别出现这些影响的鲁棒方法的应用，发现50个候选基因，这些基因被预测为原始的偏见，但是有11个独立的验证。偏见仅证实了这些新型案例中的6个。
通常表达了两个哺乳动物基因的副本，但在某些情况下，“烙印”限制了具有每个基因的两个副本的表达。它对每个性别的效用都是广泛的争论，并且具有完整的印迹基因目录及其功能对于充分表征这种现象至关重要筛选显示了大约130个印迹基因，并且发现的速度放缓表明我们正在满足两项基于RNA的高通量测序的最新研究。试图再现这些结果，我们进行了其他分析，表明大多数发现是由于实验方法和测定中的噪声用新的方法来补救这种噪声，并应用它们来识别50种新型假定的基因。
In contrast to existing estimates of approximately 200 murine imprinted genes, recent work based on transcriptome sequencing uncovered parent-of-origin allelic effects at more than 1,300 loci in the developing brain and two adult brain regions, including hundreds present in only males or females. Our independent replication of the embryonic brain stage, where the majority of novel imprinted genes were discovered and the majority of previously known imprinted genes confirmed, resulted in only 12.9% concordance among the novel imprinted loci. Further analysis and pyrosequencing-based validation revealed that the vast majority of the novel reported imprinted loci are false-positives explained by technical and biological variation of the experimental approach. We show that allele-specific expression (ASE) measured with RNA–Seq is not accurately modeled with statistical methods that assume random independent sampling and that systematic error must be accounted for to enable accurate identification of imprinted expression. Application of a robust approach that accounts for these effects revealed 50 candidate genes where allelic bias was predicted to be parent-of-origin–dependent. However, 11 independent validation attempts through a range of allelic expression biases confirmed only 6 of these novel cases. The results emphasize the importance of independent validation and suggest that the number of imprinted genes is much closer to the initial estimates. Typically both copies of mammalian genes are expressed, but in some cases, “imprinting” restricts expression to the maternal or paternal copy. Having two copies of each gene is considered advantageous since in enables compensation when one does not function properly. Why imprinting evolved and its utility to each sex is widely debated, and having a complete catalog of imprinted genes and their functions is essential for fully characterizing this phenomenon. 25 years of screening has revealed about 130 imprinted genes, and the slowing rate of discovery suggests that we are reaching saturation. Two recent studies based on high-throughput sequencing of RNA reported more than 1,300 imprinted genes. To understand the basis of this paradigm shift, we first attempted to reproduce these results. Unable to do so, we performed additional analyses that show that most of these discoveries are due to noise in the experimental approach and assay. We remedy this with new methods that account for this noise and applied them to identify 50 novel putative imprinted genes. These methods will be useful for identifying genuine novel cases of imprinted expression as this type of screening approach becomes broadly utilized.
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影响因子：
4.9
作者：
Fontanillas P;Landry CR;Wittkopp PJ;Russ C;Gruber JD;Nusbaum C;Hartl DL
通讯作者：
Hartl DL
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通讯作者：
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