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Related Concept Videos

Transcription Initiation01:47

Transcription Initiation

22.0K
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...
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Eukaryotic RNA Polymerases00:58

Eukaryotic RNA Polymerases

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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...
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Eukaryotic RNA Polymerases00:58

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Bacterial Transcription01:53

Bacterial Transcription

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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:
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Chromatin Structure Regulates pre-mRNA Processing02:41

Chromatin Structure Regulates pre-mRNA Processing

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In eukaryotic cells, nascent mRNA transcripts need to undergo many post-transcriptional modifications to reach the cell cytoplasm and translate into functional proteins. For a long time, transcription and pre-mRNA processing were considered two independent events that occur sequentially in the cell. However, it has now been well established that transcription and pre-mRNA processing are two simultaneous processes that are precisely regulated inside the cell.
The chromatin structure, especially...
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RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

11.3K
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...
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The Promoter-Proximal Pause: A Decision Point Governing RNA Polymerase II Fate.

Usman Hyder1, David L Bentley1

  • 1Department of Biochemistry and Molecular Genetics and RNA Bioscience Initiative, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, USA;

Annual Review of Biochemistry
|March 20, 2026
PubMed
Summary

RNA polymerase II (RNAPII) pausing near gene start sites acts as a crucial checkpoint. This process regulates gene expression by controlling RNAPII movement and preventing errors.

Keywords:
RNA polymerase IIpause releasepausingpremature terminationtranscription elongation

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Area of Science:

  • Molecular Biology
  • Gene Regulation
  • Biochemistry

Background:

  • Most genes in multicellular animals exhibit RNA polymerase II (RNAPII) pausing ~50 bases downstream of the transcription start site, known as promoter-proximal pausing (PPP).
  • This pausing is a critical regulatory mechanism influenced by positive and negative elongation factors that bind to RNAPII.
  • Paused RNAPII complexes can either be released into the gene body or undergo premature termination.

Purpose of the Study:

  • To elucidate the role of RNAPII dynamics at the promoter-proximal pause (PPP) site.
  • To investigate how PPP influences transcriptional quality control.
  • To understand the regulation of RNAPII flux through genes via pausing mechanisms.

Main Methods:

  • The study discusses theoretical models and existing experimental data on RNAPII behavior at the PPP.
  • Analysis of factors controlling RNAPII pausing and release.
  • Examination of the consequences of pausing on gene expression fidelity and efficiency.

Main Results:

  • RNAPII dynamics at the PPP serve as a critical quality control checkpoint for transcription.
  • Pausing regulates the rate at which RNAPII transcribes the gene body, influencing overall gene expression levels.
  • The balance between pause release and attenuation determines the fate of paused RNAPII complexes.

Conclusions:

  • A novel pause release-attenuation model is proposed to explain RNAPII dynamics at the PPP.
  • RNAPII pausing is integral to both the fidelity and regulatory control of gene transcription in multicellular organisms.
  • Understanding these dynamics is key to comprehending gene expression regulation.