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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...
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 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...
RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
Bacterial RNA Polymerase00:43

Bacterial RNA Polymerase

Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...

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Artificial RNA Polymerase II Elongation Complexes for Dissecting Co-transcriptional RNA Processing Events
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Structure of cytoplasmic RNA polymerase II.

Annamaria Hlavata1, Benjamin Neuditschko2, Ulla Schellhaas3

  • 1Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria.

Nature Communications
|July 13, 2026
PubMed
Summary

Researchers uncovered how cytoplasmic RNA polymerase II (Pol II) is assembled with key factors like GPN1 and GPN3. This process prevents errors and ensures proper gene transcription in the nucleus.

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Saccharomyces cerevisiae Metabolic Labeling with 4-thiouracil and the Quantification of Newly Synthesized mRNA As a Proxy for RNA Polymerase II Activity

Published on: October 22, 2018

Area of Science:

  • Molecular Biology
  • Structural Biology
  • Biochemistry

Background:

  • RNA polymerase II (Pol II) is essential for transcribing protein-coding genes.
  • The cytoplasmic assembly of Pol II and the roles of its biogenesis factors are not well understood.
  • Understanding Pol II assembly is crucial for comprehending gene regulation.

Purpose of the Study:

  • To determine the structure of human Pol II during cytoplasmic biogenesis.
  • To elucidate the roles of Gdown1, RPAP2, GPN1, and GPN3 in Pol II assembly.
  • To reveal the mechanism controlling the association of biogenesis factors with Pol II.

Main Methods:

  • Integrative structural analysis using cryo-electron microscopy (Cryo-EM).
  • Biochemical assays to study protein interactions and GTP hydrolysis.
  • Analysis of a native human Pol II complex from the cytoplasm.

Main Results:

  • The structure reveals how Gdown1 and RPAP2 associate with Pol II, preventing premature transcription factor binding.
  • RPAP2 tethers GPN1-GPN3 to the Pol II complex.
  • GTP hydrolysis by GPN1-GPN3 acts as a molecular switch controlling biogenesis factor association.

Conclusions:

  • A network of interactions chaperones cytoplasmic Pol II, preventing aberrant interactions during assembly.
  • A molecular switch mechanism regulates the association of biogenesis factors.
  • A general mechanism for GPN-loop GTPase function in enzyme assembly is proposed.