Quadruplex DNA in long terminal repeats of maize LTR retrotransposons

Many studies have shown that guanine-rich sequences form quadruplex DNA in vitro but there is scarce evidence of guanine quadruplex (G4) existence in vivo. A majority of potential quadruplex-forming sequences (PQS) is located in transposable elements, especially close to promoters within long terminal repeats of plant LTR retrotransposons. In order to test a potential effect of G4s on retrotransposon expression, we cloned the long terminal repeats of selected maize LTR retrotransposons upstream of lacZ reporter gene and measured its transcription and translation in yeast. We found that G4s had an inhibitory effect on translation in vivo since “mutants” (where guanines were replaced by adenines in PQS) showed higher expression levels than wild-type. In parallel, we confirmed by circular dichroism that the selected sequences can indeed adopt G4 conformation in vitro. Analysis of RNA-Seq of total RNA of maize seedlings grown in the presence of a G4-stabilizing ligand (NMM) showed both inhibitory as well as stimulatory effects on transcription of LTR retrotransposons. Our results demonstrate that quadruplex DNA is formed in vivo and plays a regulatory role in LTR retrotransposon life-cycle, thus also affecting genome dynamics.

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