Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Transcription Elongation Factors02:35

Transcription Elongation Factors

10.8K
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...
10.8K
Bacterial Transcription01:53

Bacterial Transcription

28.2K
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:
28.2K
Transcription Initiation01:47

Transcription Initiation

16.4K
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...
16.4K
Transcription Attenuation in Prokaryotes02:42

Transcription Attenuation in Prokaryotes

15.3K
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...
15.3K
RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

9.2K
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...
9.2K
Eukaryotic RNA Polymerases00:58

Eukaryotic RNA Polymerases

24.2K
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...
24.2K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Copy-back RNA synthesis by coronavirus polymerase requires helicase activity and is stimulated by remdesivir and molnupiravir.

Science advances·2026
Same author

Selective targeting of a histone-like silencer Sfx to the R6K conjugal transfer operon.

Nucleic acids research·2026
Same author

MACRO-MOLECULAR CROWDING FAVORS WRITHE IN UNWOUND DNA.

bioRxiv : the preprint server for biology·2026
Same author

Exploration of the structural and functional diversity in the metamorphic RfaH subfamily.

bioRxiv : the preprint server for biology·2026
Same author

Structure-Activity Relationship of Pseudouridimycin Focusing on the Improvement of Chemical Stability.

Journal of medicinal chemistry·2025
Same author

A post-assembly conformational change makes the SARS-CoV-2 polymerase elongation-competent.

Nucleic acids research·2025

Related Experiment Video

Updated: Jun 28, 2025

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

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

Published on: May 13, 2019

9.7K

Reciprocating RNA Polymerase batters through roadblocks.

Jin Qian1, Allison Cartee1, Wenxuan Xu1

  • 1Physics Department, Emory University, Atlanta, GA, USA.

Nature Communications
|April 12, 2024
PubMed
Summary

Escherichia coli RNA polymerase navigates protein roadblocks, with forces influencing passage. Opposing forces can surprisingly aid transit by promoting backtracking and dissociation, especially with the GreA factor.

More Related Videos

High-throughput Purification of Affinity-tagged Recombinant Proteins
07:44

High-throughput Purification of Affinity-tagged Recombinant Proteins

Published on: August 26, 2012

14.2K
Direct Restart of a Replication Fork Stalled by a Head-On RNA Polymerase
07:27

Direct Restart of a Replication Fork Stalled by a Head-On RNA Polymerase

Published on: April 29, 2010

13.6K

Related Experiment Videos

Last Updated: Jun 28, 2025

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

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

Published on: May 13, 2019

9.7K
High-throughput Purification of Affinity-tagged Recombinant Proteins
07:44

High-throughput Purification of Affinity-tagged Recombinant Proteins

Published on: August 26, 2012

14.2K
Direct Restart of a Replication Fork Stalled by a Head-On RNA Polymerase
07:27

Direct Restart of a Replication Fork Stalled by a Head-On RNA Polymerase

Published on: April 29, 2010

13.6K

Area of Science:

  • Molecular Biology
  • Biophysics

Background:

  • RNA polymerase (RNAP) must overcome protein roadblocks to synthesize full-length RNA transcripts.
  • Understanding RNAP translocation dynamics is crucial for gene expression regulation.

Purpose of the Study:

  • To investigate the real-time dynamics of Escherichia coli RNAP translocating through protein roadblocks.
  • To determine the role of external forces and the GreA factor in RNAP passage through roadblocks.

Main Methods:

  • Real-time single-molecule force measurements of RNAP translocating through lac repressor roadblocks.
  • Utilized optical tweezers to apply controlled forces.
  • Performed computational simulations to model RNAP-roadblock interactions.

Main Results:

  • Assisting forces facilitated RNAP passage, while opposing forces hindered it at low magnitudes (0.2 pN).
  • The effect of opposing forces was abolished in the presence of the transcript cleavage factor GreA.
  • Opposing forces promoted passage when RNAP backtracking rate exceeded roadblock dissociation rate, especially with GreA.

Conclusions:

  • RNAP passage through roadblocks can occur via roadblock dissociation or cycles of backtracking, recovery, and ramming.
  • Reciprocating motion may facilitate breaking protein-DNA contacts during promoter escape and elongation.
  • These mechanisms potentially enhance productive transcription in vivo.