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Related Concept Videos

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.
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Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
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RNA Polymerase II Accessory Proteins02:36

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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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Related Experiment Video

Updated: Jan 29, 2026

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution
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Measuring RNA polymerase activity genome-wide with high-resolution run-on-based methods.

Antonio Jordán-Pla1, Maria E Pérez-Martínez1, José E Pérez-Ortín1

  • 1ERI Biotecmed, Facultad de Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain.

Methods (San Diego, Calif.)
|February 5, 2019
PubMed
Summary

This review details high-throughput genomic run-on methods for studying nascent RNA. These techniques precisely map RNA polymerases during transcription, advancing our understanding of gene expression regulation.

Keywords:
ChromatinGRO-seqGenome-wideNext generation sequencingRNATranscription rate

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Area of Science:

  • Molecular Biology
  • Genomics
  • Gene Expression

Background:

  • RNA biogenesis is a complex, regulated process involving transcription factors and RNA polymerases.
  • Understanding transcription dynamics requires precise mapping of engaged RNA polymerases.
  • Genome-scale run-on based methodologies offer powerful tools for this analysis.

Purpose of the Study:

  • To review and compare high-throughput nascent RNA detection methods.
  • To highlight the utility of genomic run-on (GRO) and its variants.
  • To contextualize run-on methods with alternative approaches to studying transcription.

Main Methods:

  • Genomic run-on (GRO) and its refined variants.
  • High-throughput sequencing for genome-wide mapping.
  • Analysis of transcriptionally-engaged RNA polymerase positions.

Main Results:

  • GRO methods provide detailed insights into RNA polymerase localization during transcription.
  • These techniques are applicable across diverse organisms and biological systems.
  • Comparison of different GRO methodologies reveals specific advantages and limitations.

Conclusions:

  • Genomic run-on techniques are essential for dissecting complex RNA biogenesis.
  • Methodological advancements continue to expand the scope of transcription studies.
  • Run-on methods offer a valuable perspective on transcriptional regulation.