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 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...
General Transcription Factors01:30

General Transcription Factors

Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
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:
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 Transcription Activators02:42

Eukaryotic Transcription Activators

Transcription activators are proteins that promote the transcription of genes from DNA to RNA. In most cases, these proteins contain two separate domains ‒ a domain that binds to DNA and a domain for activating transcription; however, in some cases, a single domain is responsible for both binding and activation of transcription, as seen in the glucocorticoid receptor and MyoD.
The binding domains are capable of recognizing and interacting with regulatory sequences on the DNA. These domains are...

You might also read

Related Articles

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

Sort by
Same author

Structural basis of long-range transcription-translation coupling.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Solid-phase synthesis and biological evaluation of des-hydroxy pseudouridimycin analogs.

ACS medicinal chemistry letters·2026
Same author

A global twitter sentiment analysis model for COVID-vaccination.

Scientific reports·2026
Same author

<i>Bacillus subtilis</i> σ<sup>A</sup> and <i>Escherichia coli</i> σ<sup>70</sup> lacking σ region 1.1 are not released during transcription initiation and elongation.

Proceedings of the National Academy of Sciences of the United States of America·2025
Same author

Crystallographic Fragment Screening of the Dengue Virus Polymerase Reveals Multiple Binding Sites for the Development of Non-nucleoside Antiflavivirals.

Journal of medicinal chemistry·2025
Same author

Development of enhanced HIV-1 non-nucleoside reverse transcriptase inhibitors with improved resistance and pharmacokinetic profiles.

Science advances·2025

Related Experiment Video

Updated: May 17, 2026

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

High-throughput Purification of Affinity-tagged Recombinant Proteins

Published on: August 26, 2012

Structural basis of transcription initiation.

Yu Zhang1, Yu Feng, Sujoy Chatterjee

  • 1Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.

Science (New York, N.Y.)
|October 23, 2012
PubMed
Summary

This study reveals the crystal structures of RNA polymerase (RNAP) transcription initiation complexes. These structures detail how RNAP and sigma factor (σ) recognize promoter DNA elements for transcription initiation.

More Related Videos

Single-Molecule Imaging of EWS-FLI1 Condensates Assembling on DNA
07:05

Single-Molecule Imaging of EWS-FLI1 Condensates Assembling on DNA

Published on: September 8, 2021

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

Related Experiment Videos

Last Updated: May 17, 2026

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

High-throughput Purification of Affinity-tagged Recombinant Proteins

Published on: August 26, 2012

Single-Molecule Imaging of EWS-FLI1 Condensates Assembling on DNA
07:05

Single-Molecule Imaging of EWS-FLI1 Condensates Assembling on DNA

Published on: September 8, 2021

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

Area of Science:

  • Molecular Biology
  • Structural Biology
  • Biochemistry

Background:

  • Transcription initiation is a critical regulatory step in gene expression.
  • RNA polymerase (RNAP) forms an open complex with promoter DNA to begin transcription.
  • Understanding the structural basis of this process is key to deciphering gene regulation.

Purpose of the Study:

  • To determine the high-resolution crystal structures of functional transcription initiation complexes.
  • To elucidate the molecular interactions between RNAP, sigma factor (σ), and promoter DNA.
  • To provide insights into the mechanism of promoter recognition and DNA unwinding.

Main Methods:

  • X-ray crystallography was employed to determine the structures.
  • Functional transcription initiation complexes of Thermus thermophilus RNA polymerase, σ(A), and promoter DNA were utilized.
  • Structures were resolved at 2.9 and 3.0 Å resolution.

Main Results:

  • The crystal structures reveal specific interactions of σ with the -10 element and discriminator element, involving DNA base unstacking and pocket insertion.
  • RNAP interactions with the -4/+2 region were identified, including insertion of the +2 base into an RNAP pocket.
  • Interactions between σ and template-strand single-stranded DNA (ssDNA) were shown to preorganize the ssDNA for the RNAP active center.

Conclusions:

  • The determined structures provide a detailed molecular view of promoter recognition during transcription initiation.
  • These findings highlight the precise roles of σ and RNAP in binding and unwinding promoter DNA.
  • The study offers a structural basis for understanding how transcription initiation complexes are pre-organized for efficient DNA engagement.