Targeted RNA-seq improves efficiency, resolution, and accuracy of allele specific expression for human term placentas.
Targeted RNA-seq improves efficiency, resolution, and accuracy of allele specific expression for human term placentas.
复制标题
DOI：
10.1093/g3journal/jkab176
复制
发表时间：
2021-08-07
期刊：
影响因子：
--
通讯作者：
Vincenz C
中科院分区：
文献类型：
--
作者：
Wu W;Lovett JL;Shedden K;Strassmann BI;Vincenz C
基因组印记是一种表观遗传机制，导致等位基因特异性表达（ASE）的基础上的起源父母。已知它在哺乳动物母体资源的产前和产后分配中发挥作用。通过全转录组RNA-seq（wht-RNAseq）检测的ASE已被广泛用于使用小鼠中的相互杂交来分析印迹基因，以产生大量信息性SNP。由于SNP的缺乏以及RNA在足月胎盘和其他组织中的保存较差，人类研究更具挑战性。靶向RNA-seq（tar-RNAseq）可以通过将测序资源集中在转录组中感兴趣的区域来缓解这些挑战。在这里，我们在一项研究中比较了tar-RNAseq和wht-RNAseq在从西非马里的健康人群中收集的胎盘组织中已知印记基因的ASE。正如预期的那样，tar-RNAseq大大提高了SNP的覆盖率。与wht-RNAseq相比，tar-RNAseq在每个样本的两倍基因中产生了平均四倍多的SNP，并且SNP的读取深度增加了四倍。在以前对人类的研究中，同一基因的SNP的不一致ASE值限制了准确定量ASE的能力。我们发现，tar-RNAseq减少了这种限制，因为它意外地增加了相同基因的SNP之间ASE的一致性，即使在降解RNA的情况下。旨在发现ASE个体变异与哺乳动物和开花植物表型之间关联的研究将受益于tar-RNAseq的改进能力和准确性。
Genomic imprinting is an epigenetic mechanism that results in allele-specific expression (ASE) based on the parent of origin. It is known to play a role in the prenatal and postnatal allocation of maternal resources in mammals. ASE detected by whole transcriptome RNA-seq (wht-RNAseq) has been widely used to analyze imprinted genes using reciprocal crosses in mice to generate large numbers of informative SNPs. Studies in humans are more challenging due to the paucity of SNPs and the poor preservation of RNA in term placentas and other tissues. Targeted RNA-seq (tar-RNAseq) can potentially mitigate these challenges by focusing sequencing resources on the regions of interest in the transcriptome. Here, we compared tar-RNAseq and wht-RNAseq in a study of ASE in known imprinted genes in placental tissue collected from a healthy human cohort in Mali, West Africa. As expected, tar-RNAseq substantially improved the coverage of SNPs. Compared to wht-RNAseq, tar-RNAseq produced on average four times more SNPs in twice as many genes per sample and read depth at the SNPs increased fourfold. In previous research on humans, discordant ASE values for SNPs of the same gene have limited the ability to accurately quantify ASE. We show that tar-RNAseq reduces this limitation as it unexpectedly increased the concordance of ASE between SNPs of the same gene, even in cases of degraded RNA. Studies aimed at discovering associations between individual variation in ASE and phenotypes in mammals and flowering plants will benefit from the improved power and accuracy of tar-RNAseq.
影响因子：
3.7
作者：
Mozaffari SV;Stein MM;Magnaye KM;Nicolae DL;Ober C
通讯作者：
Ober C