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Why do some DNA sequences poison cells?

Principal Supervisor: Professor David Grainger, School of Biosciences

Co-supervisor: Pawel Grzechnik

PhD project title: Why do some DNA sequences poison cells?

University of Registration: University of Birmingham

Project outline:

Life on our planet is permitted by an ancient set of instructions encoded by DNA. Consequently, the observation that a cell can be poisoned by its own DNA is completely counterintuitive. The phenomenon results from the intrinsic toxicity of certain DNA sequences. Such sequences, initially conspicuous as being “unclonable”, are frequently rich in adenine (A) and thymine (T) bases (1). The toxicity of this “AT-rich” DNA has been documented in diverse cell types but, despite having implications for all DNA based life, a molecular explanation is lacking. The significance of toxic DNA is best understood for bacteria, where “silencing” proteins bind AT-rich sequence to nullify its effects (1). My lab’s recent focus has been to understand how these “silencing” proteins function. Our work has targeted the bacterial H-NS protein (2,3). Contrary to expectations, we have shown that a major role of H NS is to prevent spurious transcription initiating within the coding sequences of AT-rich genes (2,3,4). Thus, we propose that AT-rich DNA is toxic because it promotes spurious intragenic RNA synthesis. This is a simple consequence of RNA polymerase having a clear preference for binding AT-rich DNA. Intriguingly, this characteristic of RNA polymerase is conserved throughout life. Our project aims to understand DNA toxicity and its evolutionary conservation.


  1. Dorman, CJ. (2007) H-NS, the genome sentinel. Nat. Rev. Microbiol. 5: 157-161.
  2. Wade JT, Grainger DC. (2014) Pervasive transcription: illuminating the dark matter of bacterial transcriptomes. Nat. Rev. Microbiol. 12:647-53.
  3. Singh SS, Singh N, Bonocora RP, Fitzgerald DM, Wade JT, Grainger DC. (2014) Widespread suppression of intragenic transcription initiation by H-NS. Genes Dev. 28:214-9.
  4. Lamberte LE, Baniulyte G, Singh SS, Stringer AM, Bonocora RP, Stracy M, Kapanidis AN, Wade JT, Grainger DC. (2017) Horizontally acquired AT-rich genes in Escherichia coli cause toxicity by sequestering RNA polymerase. Nat Microbiol. 2:16249.

BBSRC Strategic Research Priority: Understanding the Rules of Life: Microbiology

Techniques that will be undertaken during the project:

  • Protein purification
  • Chromatin Immunoprecipitation
  • Illuminia Sequencing and associated bioinformatics
  • PCR
  • Radioisotopes
  • Microscopy
  • In vitro DNA binding assays
  • Reporter assays
  • Microbial cell culture
  • Mutagenesis
  • Lab based evolution

Contact: Professor David Grainger, University of Birmingham