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Related Concept Videos

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...
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...
Bacterial Transcription01:53

Bacterial Transcription

RNA polymerase (RNAP) carries out DNA-dependent RNA synthesis in both bacteria and eukaryotes. Bacteria do not have a membrane-bound nucleus. So, transcription and translation occur simultaneously, on the same DNA template.
Transcription can be divided into three main stages, each involving distinct DNA sequences to guide the polymerase. These are:
Transcription Initiation01:47

Transcription Initiation

Initiation is the first step of transcription in eukaryotes. Prokaryotic RNA Polymerase (RNAP) can bind to the template DNA and start transcribing. On the other hand, transcription in eukaryotes requires additional proteins, called transcription factors, to first bind to the promoter region in the DNA template. This binding helps recruit the specific RNAP that can assemble on the DNA and start transcription.
The promoters and enhancers and their accessory proteins allow tight regulation of...
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...
Transcriptional Regulation: Riboswitches01:23

Transcriptional Regulation: Riboswitches

Riboswitches are RNA elements that regulate gene expression by altering their secondary structures in response to specific effector molecules. These elements, located in the leader regions of certain mRNAs, act as transcriptional regulators by toggling between alternative conformations to control downstream gene expression. Riboswitch-mediated regulation is a precise mechanism for modulating biosynthetic pathways, as exemplified by the riboflavin biosynthesis pathway in Bacillus...

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Related Experiment Video

Updated: Jul 9, 2026

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

The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II.

Minkyu Kim1, Nevan J Krogan, Lidia Vasiljeva

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

Nature
|November 27, 2004
PubMed
Summary

RNA polymerase II carboxy-terminal domain phosphorylation regulates mRNA processing. The Rat1/Rai1 exonuclease degrades 3’ RNA, triggering transcription termination at polyadenylation sites.

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Last Updated: Jul 9, 2026

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

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Monitoring Protein-RNA Interaction Dynamics In Vivo at High Temporal Resolution Using χCRAC
09:15

Monitoring Protein-RNA Interaction Dynamics In Vivo at High Temporal Resolution Using χCRAC

Published on: May 9, 2020

Area of Science:

  • Molecular Biology
  • Gene Expression
  • RNA Processing

Background:

  • The carboxy-terminal domain (CTD) of RNA polymerase II (RNApII) coordinates transcription with mRNA processing through phosphorylation patterns.
  • Specific CTD phosphorylation, like serine 2, recruits polyadenylation factors essential for both mRNA processing and transcription termination.

Purpose of the Study:

  • To investigate the roles of Rtt103 and the Rat1/Rai1 exonuclease in transcription termination.
  • To elucidate the mechanism coupling polyadenylation site cleavage to RNA polymerase II transcription termination.

Main Methods:

  • Localization studies of Rtt103 and Rat1/Rai1 at gene 3' ends.
  • Analysis of RNA stability and transcription termination in mutant cells (rat1-1, rai1Delta).

Main Results:

  • Rtt103 and Rat1/Rai1 localize to the 3' ends of protein-coding genes.
  • Mutations in Rat1 or Rai1 lead to stabilization of RNA downstream of polyadenylation sites.
  • Termination defects are observed in numerous genes in the absence of functional Rat1/Rai1.

Conclusions:

  • Polyadenylation site cleavage is a prerequisite for the degradation of downstream RNA by the Rat1/Rai1 exonuclease.
  • The degradation of 3'-downstream RNA by Rat1/Rai1 is a key event that triggers transcription termination.