3’ RNA sequencing (3’ RNA-seq)

Overview

3’ RNA-seq (also called 3’-end sequencing or QuantSeq) is a strand-specific RNA sequencing approach that sequences only the 3’ end of polyadenylated transcripts. It provides gene-level expression quantification at lower cost than full-length RNA-seq and is particularly useful for FFPE and low-quality RNA samples. The Lexogen QuantSeq 3’ mRNA-Seq Library Prep FWD kit is a common implementation. Reads are biased toward the 3’ end, making it less suitable for isoform analysis or fusion detection.

Used by

  • Used in endometrial polyp genomic characterization to quantify gene expression from 25 polyps and 6 normal endometrium samples, enabling identification of HMGA1/HMGA2 rearrangement-driven expression changes including PLAG1 and ZMAT3 upregulation PMID:28445112

Notes

  • Reads are enriched toward the 3’ end of transcripts, limiting isoform-level resolution.
  • Suitable for samples with degraded RNA or FFPE material.
  • Lower per-sample cost than full-length RNA-seq makes it attractive for large cohorts.
  • Not suitable for gene fusion detection; paired full-length RNA-seq or targeted panels are required for fusions.

Sources

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