Transcription arrest at G quadruplex DNA‐forming sequences

Abstract

G quadruplex DNA is a four stranded non‐B DNA structure that can transiently form in G repeats by stacking of G quartets. G4 DNA formation has been associated with promoter regions and a functional role of this structure in gene regulation has been proposed. G4‐forming sequences also correspond with genomic regions particularly susceptible to genomic instability. Transcription has a central role in formation of these structures and in the instability associated to these sites. However, little is known about how G4 DNA is processed when encountered by an elongating RNA polymerase. Here we describe the effect of a G4 DNA‐forming sequence contained in the human c‐myb proto‐oncogene on T7 RNA polymerase (T7RNAP) transcription. This G‐rich sequence consists of three repeats of sequence (GGA)4 that fold into G4 DNA under physiological conditions. We found that this G4 forming‐sequence is a strong block to T7RNAP progression. Surprisingly, arrest is only observed when G4 DNA is located in the transcribed strand of template DNA. Consistent with formation of G4 DNA in the transcription template, T7RNAP arrest is strictly dependent on the presence of KCl, a cation required for formation and stability of G quartets. Our findings have broad implications for mechanisms of transcription regulation and mutagenesis associated with GGA repeats in vivo. (This work is supported by a Bankhead‐Coley New Investigator Grant 08BN‐07).