Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation

被引:194
作者
Gaidatzis, Dimos [1 ,2 ]
Burger, Lukas [1 ,2 ]
Florescu, Maria [1 ,2 ,3 ]
Stadler, Michael B. [1 ,2 ]
机构
[1] Friedrich Miescher Inst Biomed Res, Basel, Switzerland
[2] Swiss Inst Bioinformat, Basel, Switzerland
[3] Univ Basel, Basel, Switzerland
关键词
DIFFERENTIAL EXPRESSION ANALYSIS; PRE-MESSENGER-RNA; GENE-EXPRESSION; MAMMALIAN MICRORNAS; REVEALS; RECONSTRUCTION; LANDSCAPE; PRECISION; DYNAMICS; BINDING;
D O I
10.1038/nbt.3269
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
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.
引用
收藏
页码:722 / 729
页数:8
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