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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,...
Eukaryotic RNA Polymerases00:58

Eukaryotic RNA Polymerases

RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
All three eukaryotic RNAPs require specific transcription factors, of which the...
Termination of Translation01:44

Termination of Translation

The large ribosomal subunit has several important structures essential to translation. These include the peptidyl transferase center (PTC) - which is the site where the peptide bond is formed - and a large, internal, water-filled tube through which the nascent polypeptide moves. This latter structure is called the Peptide Exit Tunnel, and it begins at the PTC and spans the body of the large ribosomal subunit. During translation, as the nascent polypeptide chain is synthesized, it passes through...
Termination of Translation01:44

Termination of Translation

The large ribosomal subunit has several important structures essential to translation. These include the peptidyl transferase center (PTC) - which is the site where the peptide bond is formed - and a large, internal, water-filled tube through which the nascent polypeptide moves. This latter structure is called the Peptide Exit Tunnel, and it begins at the PTC and spans the body of the large ribosomal subunit. During translation, as the nascent polypeptide chain is synthesized, it passes through...
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

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Related Experiment Video

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Analysis of Termination of Transcription Using BrUTP-strand-specific Transcription Run-on (TRO) Approach
12:12

Analysis of Termination of Transcription Using BrUTP-strand-specific Transcription Run-on (TRO) Approach

Published on: March 12, 2017

Distinct pathways for snoRNA and mRNA termination.

Minkyu Kim1, Lidia Vasiljeva1, Oliver J Rando2

  • 1Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115.

Molecular Cell
|December 13, 2006
PubMed
Summary

Yeast RNA polymerase II utilizes distinct termination pathways for messenger RNA and small nucleolar RNA genes. While mRNA termination relies on polyadenylation and exonucleases, snoRNA termination involves different factors, revealing pathway flexibility.

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Analysis of Termination of Transcription Using BrUTP-strand-specific Transcription Run-on (TRO) Approach
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Area of Science:

  • Molecular Biology
  • Gene Expression Regulation
  • RNA Processing

Background:

  • Messenger RNA (mRNA) transcription termination in yeast is coupled to polyadenylation, involving cleavage factors and the Rat1/Xrn2 exonuclease for transcript degradation.
  • Small nucleolar RNAs (snoRNAs) are transcribed by RNA polymerase II but lack polyadenylation, suggesting alternative termination mechanisms.
  • Polyadenylation factors and Rat1/Xrn2 are found at snoRNA gene loci, but their roles in snoRNA termination are unclear.

Purpose of the Study:

  • To investigate the distinct transcription termination mechanisms employed for mRNA and snoRNA genes in yeast.
  • To identify the specific factors and pathways involved in snoRNA gene termination.
  • To understand the interplay between polyadenylation-dependent and -independent termination routes.

Main Methods:

  • Chromatin immunoprecipitation (ChIP) to assess the localization of polyadenylation factors and Rat1 at snoRNA genes.
  • Analysis of termination efficiency in yeast mutants affecting polyadenylation cleavage, Rat1 activity, Nrd1, Sen1, Ssu72, and the exosome complex.
  • Comparative studies of termination defects in both mRNA and snoRNA genes under various genetic conditions.

Main Results:

  • Mutations disrupting poly(A) site cleavage or Rat1/Xrn2 activity did not impair termination at snoRNA genes.
  • Nrd1, Sen1, and Ssu72 are crucial for snoRNA termination but not for termination of several tested mRNA genes.
  • The exosome complex is required for 3' end processing of snoRNAs, not for termination, while Pcf11 is essential for both pathways with differential allele effects.

Conclusions:

  • Yeast RNA polymerase II employs at least two distinct transcription termination pathways: one for polyadenylated mRNAs and another for non-polyadenylated snoRNAs.
  • The snoRNA termination pathway relies on factors like Nrd1, Sen1, and Ssu72, independent of polyadenylation.
  • RNA polymerase II maintains the capacity to utilize alternative termination strategies, providing flexibility in gene expression regulation.