Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation
Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation
复制标题
DOI：
10.1038/nbt.3269
复制
发表时间：
2015-07-01
影响因子：
46.9
通讯作者：
Stadler, Michael B.
中科院分区：
文献类型：
--
作者：
Gaidatzis, Dimos;Burger, Lukas;Stadler, Michael B.
RNA-seq实验产生的读数不仅来自成熟RNA转录物，而且来自前mRNA。在这里，我们提出了一种称为外显子-内含子分裂分析（EISA）的计算方法，该方法可以测量不同实验条件下成熟RNA和前mRNA读数的变化，以量化基因表达的转录和转录后调控。我们将EISA应用于17个不同的数据集，以表明大多数内含子读段来自核RNA，内含子读段计数的变化准确地预测转录活性的变化。此外，转录后调节的变化可以从外显子和内含子变化之间的差异来预测。EISA揭示了转录和转录后对表达变化的贡献，增加了可以从RNA-seq数据集获得的信息量。
RNA-seq experiments generate reads derived not only from mature RNA transcripts but also from pre-mRNA. Here we present a computational approach called exon-intron split analysis (EISA) that measures changes in mature RNA and pre-mRNA reads across different experimental conditions to quantify transcriptional and post-transcriptional regulation of gene expression. We apply EISA to 17 diverse data sets to show that most intronic reads arise from nuclear RNA and changes in intronic read counts accurately predict changes in transcriptional activity. Furthermore, changes in post-transcriptional regulation can be predicted from differences between exonic and intronic changes. EISA reveals both transcriptional and post-transcriptional contributions to expression changes, increasing the amount of information that can be gained from RNA-seq data sets.