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Related Concept Videos

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...
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 Elongation Factors02:35

Transcription Elongation Factors

Transcription elongation is a dynamic process that alters depending upon the sequence heterogeneity of the DNA being transcribed. Hence, it is not surprising that the elongation complex's composition also varies along the way while transcribing a gene.
The transcription elongation is regulated via pausing of RNA polymerase on several occasions during transcription. In bacteria, these halts are necessary because the transcription of DNA into mRNA is coupled to the translation of that mRNA into a...
Transcription Elongation Factors02:35

Transcription Elongation Factors

Transcription elongation is a dynamic process that alters depending upon the sequence heterogeneity of the DNA being transcribed. Hence, it is not surprising that the elongation complex's composition also varies along the way while transcribing a gene.
The transcription elongation is regulated via pausing of RNA polymerase on several occasions during transcription. In bacteria, these halts are necessary because the transcription of DNA into mRNA is coupled to the translation of that mRNA into a...

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Related Experiment Video

Updated: Jun 6, 2026

Monitoring eIF4F Assembly by Measuring eIF4E-eIF4G Interaction in Live Cells
08:47

Monitoring eIF4F Assembly by Measuring eIF4E-eIF4G Interaction in Live Cells

Published on: May 1, 2020

Nanometer-scale RNA protein clusters (RPCs) Foster Helicase Activity of DEAD-box eIF4A.

Him Shweta1,2, Masaaki Sokabe2, Nancy Villa2

  • 1Department of Pharmacology, University of California, Davis, CA, USA.

Biorxiv : the Preprint Server for Biology
|June 5, 2026
PubMed
Summary
This summary is machine-generated.

DEAD-box RNA helicases, like eukaryotic initiation factor 4A (eIF4A), form RNA-protein clusters (RPCs) with cofactors. This clustering is essential for efficient helicase activity in translation initiation.

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Last Updated: Jun 6, 2026

Monitoring eIF4F Assembly by Measuring eIF4E-eIF4G Interaction in Live Cells
08:47

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Published on: May 1, 2020

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10:59

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

Published on: May 13, 2019

Nanomanipulation of Single RNA Molecules by Optical Tweezers
06:59

Nanomanipulation of Single RNA Molecules by Optical Tweezers

Published on: August 20, 2014

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Structural Biology

Background:

  • DEAD-box RNA helicases regulate RNA metabolism through ATP-dependent mechanisms.
  • Eukaryotic initiation factor 4A (eIF4A) is a key translation initiation helicase that requires cofactors for activity.
  • The coordination between helicase catalysis and multi-subunit interactions is not fully understood.

Purpose of the Study:

  • To investigate the role of RNA-protein interactions in eIF4A helicase activity.
  • To uncover the structural organization of eIF4A with its cofactors and RNA.
  • To determine the functional significance of RNA-protein clustering in translation initiation.

Main Methods:

  • Single-molecule imaging to observe RNA-protein cluster formation.
  • Biochemical assays to measure helicase activity in vitro.
  • In-cell diffusion measurements using mutants to assess cluster formation in vivo.

Main Results:

  • eIF4A forms nanometer-scale RNA-protein clusters (RPCs) with cofactors eIF4B, eIF4G, RNA, and ATP.
  • RPC formation is dependent on ATP and correlates with enhanced helicase activity.
  • eIF4B is crucial for assembly, with its disordered regions and RRMs driving multivalent clustering.
  • Disrupting eIF4B-RNA interactions reduces cluster size and helicase activity.
  • Wild-type eIF4B shows slower diffusion in cells compared to a mutant, indicating in-cell RPC formation.

Conclusions:

  • Regulated helicase clustering is a novel characteristic of the translation initiation machinery.
  • ATP-dependent DEAD-box helicase activity is linked to nanometer-scale RNA-protein clusters.
  • These findings provide new insights into the regulation of translation initiation.