Defining data-driven primary transcript annotations with primaryTranscriptAnnotation in R
Defining data-driven primary transcript annotations with primaryTranscriptAnnotation in R
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DOI：
10.1093/bioinformatics/btaa011
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发表时间：
2020-05-01
期刊：
影响因子：
5.8
通讯作者：
Guertin, Michael J.
中科院分区：
文献类型：
--
作者：
Anderson, Warren D.;Duarte, Fabiana M.;Guertin, Michael J.
摘要：来自连续测序实验的新生转录测量对于转录机制和调控网络的研究至关重要。然而，传统的mRNA基因注释与初级转录本的边界有很大的不同。需要新的主要成绩单注释来准确解释运行数据。我们开发了PrimiyTranscriptAnnotation R程序包，用于从基因组运行数据中推断初级转录本的转录起始和终止位置。然后我们使用这些推断的坐标来注释识别出从头开始的转录单位。这个包提供了一种新的实用程序，可以将数据驱动的初级转录注释与以无偏见方式识别的转录单位坐标整合在一起。强调使用准确的初级转录本坐标的重要性，我们证明了这种新的方法增加了差异表达转录本的检测，并提供了更准确的RNA聚合酶暂停指数的量化。
aSummary: Nascent transcript measurements derived from run-on sequencing experiments are critical for the investigation of transcriptional mechanisms and regulatory networks. However, conventional mRNA gene annotations significantly differ from the boundaries of primary transcripts. New primary transcript annotations are needed to accurately interpret run-on data. We developed the primaryTranscriptAnnotation R package to infer the transcriptional start and termination sites of primary transcripts from genomic run-on data. We then used these inferred coordinates to annotate transcriptional units identified de novo. This package provides the novel utility to integrate data-driven primary transcript annotations with transcriptional unit coordinates identified in an unbiased manner. Highlighting the importance of using accurate primary transcript coordinates, we demonstrate that this new methodology increases the detection of differentially expressed transcripts and provides more accurate quantification of RNA polymerase pause indices.