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RNA Polymerase II Accessory Proteins

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 Proteins

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 Polymerases

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 Polymerases

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...

The Replisome

The Replisome

DNA replication is carried out by a large complex of proteins that act in a coordinated matter to achieve high-fidelity DNA replication. Together this complex is known as the DNA replication machinery or the replisome.
The synthesis of the leading and lagging strands is a highly coordinated process. To explain this, the “Trombone model” was proposed by Bruce Alberts in 1980. The DNA loop formation starts when a primer is synthesized on the parent lagging strand. The loop grows with the...

The Replisome

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DNA replication is carried out by a large complex of proteins that act in a coordinated matter to achieve high-fidelity DNA replication. Together this complex is known as the DNA replication machinery or the replisome.
The synthesis of the leading and lagging strands is a highly coordinated process. To explain this, the “Trombone model” was proposed by Bruce Alberts in 1980. The DNA loop formation starts when a primer is synthesized on the parent lagging strand. The loop grows with the...

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Related Experiment Video

Updated: Jun 13, 2026

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

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

Published on: May 13, 2019

Structural Dynamics of RNA Polymerase II During Nucleotide Addition Cycle.

Gangshun Yi^1,2, Qingrong Li³, Hannah Holmberg⁴

¹Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK.

Biorxiv : the Preprint Server for Biology

|June 12, 2026

Summary

This study reveals the complete molecular mechanism of RNA polymerase II (RNAPII) nucleotide addition cycles (NACs) using cryo-EM. It captures key transition states, providing a dynamic view of gene expression.

Keywords:

Cryo-EM RNA polymerase Transcription affinity grids allosteric regulation structural biology structural dynamics: dynamic conformational change transcription elongation trigger loop

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Last Updated: Jun 13, 2026

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

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Published on: May 13, 2019

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Published on: August 26, 2012

Chemical Triphosphorylation of Oligonucleotides

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Published on: June 2, 2022

Area of Science:

Molecular Biology
Structural Biology
Biochemistry

Background:

RNA polymerase II (RNAPII) is essential for gene expression via nucleotide addition cycles (NACs).
Previous studies lacked detailed structural insights into pre- and post-catalysis intermediates of the NAC.
Understanding these dynamics is crucial for deciphering gene regulation.

Purpose of the Study:

To elucidate the complete mechanistic pathway of the RNAPII NAC.
To capture and characterize transient structural intermediates of the RNAPII elongation complex (EC).
To provide a dynamic framework for RNAPII function.

Main Methods:

Utilized cryo-electron microscopy (cryo-EM) to obtain 43 distinct structures of the yeast *S. cerevisiae* RNAPII EC.
Captured previously unobserved transition intermediates within the NAC.
Analyzed structural dynamics across the entire NAC.

Main Results:

Established a continuous spectrum of RNAPII EC structural dynamics during the NAC.
Identified two coordinated phases: substrate-induced tightening and post-catalysis relaxation.
Captured the short-lived post-catalysis product state and intermediates facilitating translocation.
Observed allosteric conformational changes upon substrate binding, including TL folding and clamp closure.

Conclusions:

Defined a comprehensive structural and dynamic framework for the RNAPII NAC.
Generated a "molecular movie" of RNAPII in action.
Revealed how RNAPII balances speed and fidelity through coordinated conformational dynamics.