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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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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.
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DNA replication is initiated at sites containing predefined DNA sequences known as origins of replication. DNA is unwound at these sites by the minichromosome maintenance (MCM) helicase and other factors such as Cdc45 and the associated GINS complex.The unwound single strands are protected by replication protein A (RPA) until DNA polymerase starts synthesizing DNA at the 5’ end of the strand in the same direction as the replication fork. To prevent the replication fork from falling apart,...
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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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Related Experiment Video

Updated: Nov 10, 2025

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

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Conserved DNA sequence features underlie pervasive RNA polymerase pausing.

Martyna Gajos1,2, Olga Jasnovidova1, Alena van Bömmel2,3

  • 1Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany.

Nucleic Acids Research
|March 31, 2021
PubMed
Summary
This summary is machine-generated.

Researchers discovered widespread RNA polymerase II pausing throughout the human genome, primarily within gene bodies, not just near promoters. This sequence-driven pausing, conserved across species, offers new insights into gene expression regulation.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Gene Regulation

Background:

  • RNA polymerase II (Pol II) pausing is a known regulatory mechanism in gene expression.
  • Previous studies primarily focused on promoter-proximal pausing in metazoans, leaving the genome-wide prevalence and regulatory role in mammalian cells unclear.

Purpose of the Study:

  • To investigate the genome-wide distribution and characteristics of RNA polymerase II pausing in human cells.
  • To develop novel computational and sequencing methods for accurate detection of transcriptional pausing.

Main Methods:

  • Development of a pause detecting algorithm (PDA) for nucleotide-resolution occupancy data.
  • Implementation of nested native elongating transcript sequencing (NET-seq) to minimize artifactual pausing signals.
  • Genome-wide analysis of Pol II pausing sites and associated DNA sequence properties using machine learning.

Main Results:

  • Widespread, genome-wide RNA polymerase II pausing detected at single-nucleotide resolution in human cells.
  • The majority of Pol II pauses occur within the gene body, rather than promoter-proximal regions.
  • Identification of novel DNA sequence motifs associated with transcriptional pausing, conserved between human cells and bacteria.

Conclusions:

  • Transcriptional pausing is a pervasive, sequence-induced phenomenon across the human genome.
  • The precise location of pausing suggests significant, yet uncharacterized, functional roles in gene expression regulation.
  • The findings provide a foundation for understanding the regulatory potential of widespread transcriptional pausing.