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Related Experiment Video

Updated: May 2, 2026

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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RHAPA: a new method to quantify alternative polyadenylation.

Ashley L Cornett1, Carol S Lutz

  • 1Department of Biochemistry and Molecular Biology, Graduate School of Biomedical Sciences, New Jersey Medical School, Rutgers, The State University of New Jersey, 185 South Orange Avenue, Newark, NJ, 07103, USA.

Methods in Molecular Biology (Clifton, N.J.)
|March 5, 2014
PubMed
Summary
This summary is machine-generated.

Researchers developed a new method, RNase H alternative polyadenylation assay (RHAPA), to quantify alternative polyadenylation in messenger RNAs (mRNAs). This technique measures different mRNA transcript variants, aiding the study of gene expression regulation.

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • Messenger RNA (mRNA) 3' end formation is crucial for mRNA stability, turnover, and translation.
  • Polyadenylation involves mRNA cleavage and addition of poly(A) tails, with alternative polyadenylation producing multiple transcript variants.

Purpose of the Study:

  • To introduce and validate a novel method for directly measuring and quantifying alternatively polyadenylated transcripts.
  • To enable the examination of poly(A) signal selection across different cellular conditions and types.

Main Methods:

  • Development of the RNase H alternative polyadenylation assay (RHAPA).
  • RHAPA utilizes conventional RT-PCR, gene-specific oligonucleotide hybridization, and RNase H cleavage.
  • The method provides absolute quantification of individual transcript variants.

Main Results:

  • RHAPA successfully measures and quantifies alternatively polyadenylated transcripts.
  • The assay allows for direct assessment of transcript variant expression levels.
  • Demonstrated utility in examining poly(A) signal usage under varying conditions.

Conclusions:

  • RHAPA is an effective tool for analyzing alternative polyadenylation.
  • This method advances the study of posttranscriptional gene regulation.
  • RHAPA facilitates a deeper understanding of mRNA processing and its impact on gene expression.