Mapping 3' mRNA isoforms on a genomic scale

Yi Jin, Joseph V. Geisberg, Zarmik Moqtaderi, Zhe Ji, Mainul Hoque, Bin Tian, Kevin Struhl

Research output: Contribution to journalArticlepeer-review

14 Scopus citations


Most eukaryotic genes are transcribed into mRNAs with alternative poly(A) sites. Emerging evidence suggests that mRNA isoforms with alternative poly(A) sites can perform critical regulatory functions in numerous biological processes. In recent years, a number of strategies utilizing high-throughput sequencing technologies have been developed to aid in the identification of genome-wide poly(A) sites. This unit describes a modified protocol for a recently published 3'READS (3' region extraction and deep sequencing) method that accurately identifies genome-wide poly(A) sites and that can be used to quantify the relative abundance of the resulting 3' mRNA isoforms. This approach minimizes nonspecific sequence reads due to internal priming and typically yields a high percentage of sequence reads that are ideally suited for accurate poly(A) identification.

Original languageEnglish (US)
Pages (from-to)4.23.1-4.23.17
JournalCurrent Protocols in Molecular Biology
StatePublished - 2015


  • 3'
  • Poly(A) sites
  • Polyadenylation
  • RNA sequencing
  • mRNA isoforms

ASJC Scopus subject areas

  • Molecular Biology


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