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Related Concept Videos

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 RNA Polymerases00:58

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 Polymerases00:58

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...
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...
Cell Specific Gene Expression01:58

Cell Specific Gene Expression

Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...

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Artificial RNA Polymerase II Elongation Complexes for Dissecting Co-transcriptional RNA Processing Events
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Gene-specific RNA polymerase II phosphorylation and the CTD code.

Hyunmin Kim1, Benjamin Erickson, Weifei Luo

  • 1Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA.

Nature Structural & Molecular Biology
|September 14, 2010
PubMed
Summary

The RNA polymerase II CTD phosphorylation code is gene-specific, influenced by promoters and affecting transcription. Ser7 phosphorylation links to splicing and termination factor Nrd1 recruitment.

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • RNA polymerase II C-terminal domain (CTD) phosphorylation is crucial for transcription and mRNA processing.
  • The CTD phosphorylation 'code' is hypothesized to regulate these processes.
  • Understanding this code's gene-specific variations is essential.

Purpose of the Study:

  • To investigate the genome-wide patterns of CTD phosphorylation (Ser2, Ser5, Ser7) in budding yeast.
  • To map the distribution of termination factors Nrd1 and Pcf11 in relation to CTD phosphorylation.
  • To elucidate how CTD phosphorylation acts as a gene-specific code.

Main Methods:

  • Genome-wide mapping of CTD Ser2, Ser5, and Ser7 phosphorylations.
  • Chromatin immunoprecipitation to map Nrd1 and Pcf11.
  • Analysis of phosphorylation patterns in relation to gene expression, length, and promoter features.

Main Results:

  • CTD phosphorylation dynamics are gene-specific, not scaled by gene length.
  • High Ser5 and Ser7 phosphorylation occurs at the 5' ends of highly expressed genes with nucleosome-occupied promoters.
  • CTD kinases Kin28 and Ctk1 influence Pol II distribution in a gene-specific manner.
  • Ser7 phosphorylation is enriched on introns and near Nrd1 binding sites, suggesting roles in splicing and termination.
  • Nrd1 and Pcf11 often colocalize.
  • Pcf11 is unexpectedly found at centromeres and on Pol III-transcribed genes.

Conclusions:

  • The CTD phosphorylation code varies significantly between genes, likely controlled by promoter elements.
  • Ser7 phosphorylation plays a role in coordinating transcription, splicing, and termination.
  • Nrd1 and Pcf11 may have overlapping functions in transcription termination.
  • Pcf11 has roles beyond Pol II transcription, including at centromeres and Pol III genes.