When push comes to shove - RNA polymerase and DNA-bound protein roadblocks

Nan Hao; Alana J Donnelly; Ian B Dodd; Keith E Shearwin

doi:10.1007/s12551-023-01064-7

When push comes to shove - RNA polymerase and DNA-bound protein roadblocks

Biophys Rev. 2023 Jun 10;15(3):355-366. doi: 10.1007/s12551-023-01064-7. eCollection 2023 Jun.

Authors

Nan Hao¹, Alana J Donnelly¹, Ian B Dodd¹, Keith E Shearwin¹

Affiliation

¹ Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005 Australia.

Abstract

In recent years, transcriptional roadblocking has emerged as a crucial regulatory mechanism in gene expression, whereby other DNA-bound obstacles can block the progression of transcribing RNA polymerase (RNAP), leading to RNAP pausing and ultimately dissociation from the DNA template. In this review, we discuss the mechanisms by which transcriptional roadblocks can impede RNAP progression, as well as how RNAP can overcome these obstacles to continue transcription. We examine different DNA-binding proteins involved in transcriptional roadblocking and their biophysical properties that determine their effectiveness in blocking RNAP progression. The catalytically dead CRISPR-Cas (dCas) protein is used as an example of an engineered programmable roadblock, and the current literature in understanding the polarity of dCas roadblocking is also discussed. Finally, we delve into a stochastic model of transcriptional roadblocking and highlight the importance of transcription factor binding kinetics and its resistance to dislodgement by an elongating RNAP in determining the strength of a roadblock.

Keywords: CRISPR; DNA binding kinetics; RNA polymerase; Transcriptional interference; Transcriptional roadblocking.

Publication types

Review