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

ABSTRACT: Convergent promoters exert transcriptional interference (TI) by several mechanisms including promoter occlusion, where elongating RNA polymerases (RNAPs) block access to a promoter. Here, we tested whether pausing of RNAPs by obstructive DNA-bound proteins can enhance TI by promoter occlusion. Using the Lac repressor as a 'roadblock' to induce pausing over a target promoter, we found only a small increase in TI, with mathematical modelling suggesting that rapid termination of the stalled RNAP was limiting the occlusion effect. As predicted, the roadblock-enhanced occlusion was significantly increased in the absence of the Mfd terminator protein. Thus, protein roadblocking of RNAP may cause pause-enhanced occlusion throughout genomes, and the removal of stalled RNAP may be needed to minimize unwanted TI.

SUBMITTER: Hao N

PROVIDER: S-EPMC6593788 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature

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

Hao Nan N Crooks Michael T MT Palmer Adam C AC Dodd Ian B IB Shearwin Keith E KE

FEBS letters 20190329 9

Convergent promoters exert transcriptional interference (TI) by several mechanisms including promoter occlusion, where elongating RNA polymerases (RNAPs) block access to a promoter. Here, we tested whether pausing of RNAPs by obstructive DNA-bound proteins can enhance TI by promoter occlusion. Using the Lac repressor as a 'roadblock' to induce pausing over a target promoter, we found only a small increase in TI, with mathematical modelling suggesting that rapid termination of the stalled RNAP wa ...[more]

PMID: 30892685

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