title: The role of repressor kinetics in relief of transcriptional interference between convergent promoters.
abstract: Transcriptional interference (TI), where transcription from a promoter is inhibited by the activity of other promoters in its vicinity on the same DNA, enables transcription factors to regulate a target promoter indirectly, inducing or relieving TI by controlling the interfering promoter. For convergent promoters, stochastic simulations indicate that relief of TI can be inhibited if the repressor at the interfering promoter has slow binding kinetics, making it either sensitive to frequent dislodgement by elongating RNA polymerases (RNAPs) from the target promoter, or able to be a strong roadblock to these RNAPs. In vivo measurements of relief of TI by CI or Cro repressors in the bacteriophage λ PR-PRE system show strong relief of TI and a lack of dislodgement and roadblocking effects, indicative of rapid CI and Cro binding kinetics. However, repression of the same λ promoter by a catalytically dead CRISPR Cas9 protein gave either compromised or no relief of TI depending on the orientation at which it binds DNA, consistent with dCas9 being a slow kinetics repressor. This analysis shows how the intrinsic properties of a repressor can be evolutionarily tuned to set the magnitude of relief of TI.
authors.affiliation: Discipline of Biochemistry, Department of Molecular and Cellular Biology, The University of Adelaide, Adelaide, South Australia 5005, Australia nan.hao@adelaide.edu.au.
authors.forename: Nan
authors.identifier: 0000-0001-5836-3507
authors.initials: N
authors.lastname: Hao
authors.affiliation: Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA.
authors.forename: Adam C
authors.identifier: 0000-0001-5028-7028
authors.initials: AC
authors.lastname: Palmer
authors.affiliation: Discipline of Biochemistry, Department of Molecular and Cellular Biology, The University of Adelaide, Adelaide, South Australia 5005, Australia.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Ahlgren-Berg
authors.affiliation: Discipline of Biochemistry, Department of Molecular and Cellular Biology, The University of Adelaide, Adelaide, South Australia 5005, Australia keith.shearwin@adelaide.edu.au.
authors.forename: Keith E
authors.initials: KE
authors.lastname: Shearwin
authors.affiliation: Discipline of Biochemistry, Department of Molecular and Cellular Biology, The University of Adelaide, Adelaide, South Australia 5005, Australia.
authors.forename: Ian B
authors.initials: IB
authors.lastname: Dodd
mesh_terms: D010582:Bacteriophage lambda; D064130:CRISPR-Associated Proteins / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D007700:Kinetics; D008958:Models, Molecular; D011401:Promoter Regions, Genetic; D012097:Repressor Proteins / Q000378:metabolism*; D013269:Stochastic Processes; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic; D054334:Viral Regulatory and Accessory Proteins / Q000378:metabolism*
chemical_list: D064130:CRISPR-Associated Proteins; D012097:Repressor Proteins; D014157:Transcription Factors; D054334:Viral Regulatory and Accessory Proteins; C016649:phage repressor proteins; D012321:DNA-Directed RNA Polymerases