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Related Concept Videos

Nonsense-mediated mRNA Decay02:27

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 Decay02:27

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,...
mRNA Stability and Gene Expression02:51

mRNA Stability and Gene Expression

The structure and stability of mRNA molecules regulates gene expression, as mRNAs are a key step in the pathway from gene to protein. In eukaryotes, the half-life of mRNA varies from a few minutes up to several days. mRNA stability is essential in growth and development. The absence of the proteins regulating its stability, such as tristetraprolin in mice, can cause systemic issues, including bone marrow overgrowth, inflammation, and autoimmunity.
Cis-acting Elements involved in mRNA stability
Transcription Attenuation in Prokaryotes02:42

Transcription Attenuation in Prokaryotes

Transcriptional attenuation occurs when RNA transcription is prematurely terminated due to the formation of a terminator mRNA hairpin structure.  Bacteria use these hairpins to regulate the transcription process and control the synthesis of several amino acids including histidine, lysine, threonine, and phenylalanine. Transcription attenuation takes place in the non-coding regions of mRNA.
There are several different mechanisms used to attenuate transcription. In ribosome mediated...
Chromatin Structure Regulates pre-mRNA Processing02:41

Chromatin Structure Regulates pre-mRNA Processing

In eukaryotic cells, nascent mRNA transcripts need to undergo many post-transcriptional modifications to reach the cell cytoplasm and translate into functional proteins. For a long time, transcription and pre-mRNA processing were considered two independent events that occur sequentially in the cell. However, it has now been well established that transcription and pre-mRNA processing are two simultaneous processes that are precisely regulated inside the cell.
The chromatin structure, especially...
RNA Interference01:23

RNA Interference

RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...

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Related Experiment Video

Updated: Jun 30, 2026

Using SecM Arrest Sequence as a Tool to Isolate Ribosome Bound Polypeptides
09:42

Using SecM Arrest Sequence as a Tool to Isolate Ribosome Bound Polypeptides

Published on: June 19, 2012

Sequence-encoded autoinhibition couples mRNA decapping activity to phase separation.

Trase Aguigam1,2, Katarzyna Grab3,4, Joanna Kowalska3

  • 1Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA.

Biorxiv : the Preprint Server for Biology
|June 29, 2026
PubMed
Summary
This summary is machine-generated.

Fission yeast Dcp2

Keywords:
Dcp1/Dcp2autoinhibitionbiomolecular condensatesintrinsically disordered regionsmRNA decappingsequence motifs

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An Oligonucleotide-based Tandem RNA Isolation Procedure to Recover Eukaryotic mRNA-Protein Complexes
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Last Updated: Jun 30, 2026

Using SecM Arrest Sequence as a Tool to Isolate Ribosome Bound Polypeptides
09:42

Using SecM Arrest Sequence as a Tool to Isolate Ribosome Bound Polypeptides

Published on: June 19, 2012

Artificial RNA Polymerase II Elongation Complexes for Dissecting Co-transcriptional RNA Processing Events
10:59

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An Oligonucleotide-based Tandem RNA Isolation Procedure to Recover Eukaryotic mRNA-Protein Complexes
09:45

An Oligonucleotide-based Tandem RNA Isolation Procedure to Recover Eukaryotic mRNA-Protein Complexes

Published on: August 18, 2018

Area of Science:

  • Molecular Biology
  • Biochemistry
  • RNA Biology

Background:

  • Messenger RNA (mRNA) decapping by the Dcp1/Dcp2 complex initiates degradation.
  • Regulatory mechanisms controlling Dcp1/Dcp2 complex activity are not fully understood.
  • The 5' cap structure is crucial for mRNA stability and translation initiation.

Purpose of the Study:

  • To investigate the regulatory mechanisms of the Dcp1/Dcp2 decapping complex.
  • To identify specific protein regions and interactions that control Dcp2 activity.
  • To understand how Dcp2 functions within phase-separated biomolecular condensates.

Main Methods:

  • Site-directed mutagenesis of fission yeast Dcp2.
  • Biochemical assays measuring decapping activity and RNA binding.
  • Analysis of protein behavior within phase-separated condensates.

Main Results:

  • Identified inhibitory motifs in the Dcp2 C-terminus that repress catalytic activity.
  • Mutations relieving autoinhibition enhanced RNA binding and bypassed the need for the activator Edc3.
  • Dcp2 activation within phase-separated condensates is maintained, showing propagation of conformational changes.
  • Long-range interactions between the Dcp2 intrinsically disordered region and its catalytic core restrict RNA binding.

Conclusions:

  • Sequence-encoded elements in the Dcp2 C-terminus allosterically regulate its catalytic activity.
  • Intrinsically disordered regions play a key role in modulating enzyme function within biomolecular condensates.
  • Understanding these regulatory mechanisms provides insights into mRNA decay pathways and protein function in condensates.