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

Methods Enzymol. 2021:655:205-223. doi: 10.1016/bs.mie.2021.03.016. Epub 2021 Apr 28.


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:

Keywords: 3′ mRNA sequencing; 3′GAmES; Alternative polyadenylation; Gene annotation; Gene expression; RNA sequencing; Transcriptomics; mRNA 3′ end formation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Gene Expression Profiling
  • High-Throughput Nucleotide Sequencing
  • Molecular Sequence Annotation
  • Polyadenylation*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Sequence Analysis, RNA
  • Transcriptome*


  • RNA, Messenger