Systematic refinement of gene annotations by parsing mRNA 3' end sequencing datasets

Pooja Bhat, Thomas R Burkard, Veronika A Herzog, Andrea Pauli, Stefan L Ameres

Publications: Contribution to bookChapter

Abstract

Alternative cleavage and polyadenylation generates mRNA 3' isoforms in a cell type-specific manner. Due to finite available RNA sequencing data of organisms with vast cell type complexity, currently available gene annotation resources are incomplete, which poses significant challenges to the comprehensive interpretation and quantification of transcriptomes. In this chapter, we introduce 3'GAmES, a stand-alone computational pipeline for the identification and quantification of novel mRNA 3'end isoforms from 3'mRNA sequencing data. 3'GAmES expands available repositories and improves comprehensive gene-tag counting by cost-effective 3' mRNA sequencing, faithfully mirroring whole-transcriptome RNAseq measurements. By employing R and bash shell scripts (assembled in a Singularity container) 3'GAmES systematically augments cell type-specific 3' ends of RNA polymerase II transcripts and increases the sensitivity of quantitative gene expression profiling by 3' mRNA sequencing. Public access: https://github.com/AmeresLab/3-GAmES.git.

Original languageEnglish
Title of host publicationmRNA 3' End Processing and Metabolism
EditorsBin Tian
Place of PublicationCambridge
PublisherAcademic Press
Chapter10
Pages205-223
Number of pages19
ISBN (Print)9780128235737
DOIs
Publication statusPublished - 2021

Publication series

SeriesMethods in Enzymology
Volume655
ISSN0076-6879

Austrian Fields of Science 2012

  • 106005 Bioinformatics
  • 106023 Molecular biology

Keywords

  • Gene Expression Profiling
  • High-Throughput Nucleotide Sequencing
  • Molecular Sequence Annotation
  • Polyadenylation
  • RNA, Messenger/genetics
  • Sequence Analysis, RNA
  • Transcriptome
  • RNA sequencing
  • mRNA 3′ end formation
  • 3′GAmES
  • Gene expression
  • Alternative polyadenylation
  • Transcriptomics
  • 3′ mRNA sequencing
  • Gene annotation

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