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Nonsense-mediated mRNA Decay

Nonsense-mediated mRNA Decay

The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...

Nonsense-mediated mRNA Decay

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The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...

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Related Experiment Video

Updated: May 22, 2026

Measurement of mRNA Decay Rates in Saccharomyces cerevisiae Using rpb1-1 Strains

Measurement of mRNA Decay Rates in Saccharomyces cerevisiae Using rpb1-1 Strains

Published on: December 13, 2014

A new function of ROD1 in nonsense-mediated mRNA decay.

T F Brazão¹, J Demmers, W van IJcken

¹Department of Cell Biology & Genetics, Erasmus MC, Rotterdam, The Netherlands. t.brazao@erasmusmc.nl

|May 12, 2012

Summary

This summary is machine-generated.

ROD1, a paralog of polypyrimidine tract binding protein (PTBP), functions in nonsense-mediated mRNA decay (NMD). ROD1 interacts with UPF1 and regulates NMD targets, revealing a new role for PTBP paralogs in gene expression control.

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Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing (RIPiT-Seq)

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Area of Science:

Molecular Biology
Gene Regulation
RNA Processing

Background:

RNA-binding proteins regulate gene expression post-transcriptionally.
Polypyrimidine tract binding protein (PTBP) is a known splicing factor.
ROD1 is a PTBP paralog with four RNA recognition motif (RRM) domains.

Purpose of the Study:

To investigate the function of ROD1 in gene expression regulation.
To determine ROD1's role in nonsense-mediated mRNA decay (NMD).

Main Methods:

Protein-protein interaction studies (e.g., co-immunoprecipitation).
Reporter assays to assess mRNA destabilization.
RNA immunoprecipitation sequencing (RIP-seq) to identify target transcripts.

Main Results:

ROD1 interacts with the core NMD factor UPF1.
ROD1 and UPF1 co-regulate a large set of target genes.
ROD1 is essential for the destabilization of NMD substrates, similar to UPF1 and UPF2.
ROD1 and UPF1 bind to a substantial number of common transcripts.

Conclusions:

ROD1 plays a significant role in nonsense-mediated mRNA decay (NMD).
ROD1 acts in concert with UPF1 to regulate NMD pathway targets.
This study uncovers a novel function for PTBP paralogs in mRNA decay and gene regulation.