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RNA polymerase pausing at a protein roadblock can enhance transcriptional interference by promoter occlusion

Nan Hao1,2, Michael T Crooks1, Adam C Palmer3

  • 1Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, Australia.

FEBS Letters
|March 21, 2019
PubMed

Insights

Transcriptional interference (TI) can be enhanced by pausing RNA polymerases (RNAPs) using DNA-binding proteins. Removing the Mfd terminator protein significantly increased this pause-enhanced occlusion, suggesting a mechanism for genome-wide TI.

Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • Convergent promoters can cause transcriptional interference (TI).
  • One mechanism is promoter occlusion, where elongating RNA polymerases (RNAPs) block promoter access.
  • The role of RNAP pausing in enhancing TI via occlusion is not fully understood.

Purpose of the Study:

  • To investigate if pausing of RNAPs by obstructive DNA-bound proteins can enhance TI through promoter occlusion.
  • To determine the role of the Mfd terminator protein in this process.

Main Methods:

  • Utilized the Lac repressor as a 'roadblock' to induce RNAP pausing over a target promoter.
  • Employed mathematical modeling to analyze the dynamics of RNAP stalling and termination.
  • Assessed TI levels in the presence and absence of the Mfd terminator protein.

Main Results:

  • A small increase in TI was observed when RNAPs were paused by the Lac repressor.
  • Mathematical modeling indicated that rapid termination of stalled RNAPs limited the occlusion effect.
  • Absence of the Mfd terminator protein significantly increased the roadblock-enhanced occlusion.

Conclusions:

  • Protein-induced RNAP pausing can enhance TI via promoter occlusion.
  • The Mfd terminator protein plays a role in resolving stalled RNAPs and mitigating TI.
  • This mechanism of pause-enhanced occlusion may operate genome-wide, and Mfd-mediated removal of stalled RNAPs is crucial for minimizing unwanted TI.
Keywords:
RNAP pausingbacteriophagemathematical modellingpromoter occlusiontranscriptional interferencetranscriptional roadblocking

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