Defining data-driven primary transcript annotations with primaryTranscriptAnnotation in R

Abstract

Nascent transcript measurements derived from run-on sequencing experiments are critical for the investigation of transcriptional mechanisms and regulatory networks. However, conventional gene annotations specify the boundaries of mRNAs, which significantly differ from the boundaries of primary transcripts. Moreover, transcript isoforms with distinct transcription start and end coordinates can vary between cell types. Therefore, 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 annotated genes from genomic run-on data. We then used these inferred co-ordinates to annotate transcriptional units identified de novo. Hence, this package provides the novel utility to integrate data-driven primary transcript annotations with transcriptional unit coordinates identified in an unbiased manner. Our analyses demonstrated that this new methodology increases the sensitivity for detecting differentially expressed transcripts and provides more accurate quantification of RNA polymerase pause indices, consistent with the importance of using accurate primary transcript coordinates for interpreting genomic nascent transcription data.Availabilityhttps://github.com/WarrenDavidAnderson/genomicsRpackage/tree/master/primaryTranscriptAnnotation