Abstract
BackgroundMany studies have shown that guanine-rich DNA sequences form quadruplex structures (G4) in vitro but there is scarce evidence of guanine quadruplexes in vivo. The majority of potential quadruplex-forming sequences (PQS) are located in transposable elements (TEs), especially close to promoters within long terminal repeats of plant LTR retrotransposons.ResultsIn order to test the potential effect of G4s on retrotransposon expression, we cloned the long terminal repeats of selected maize LTR retrotransposons upstream of the 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-types. In parallel, we confirmed by circular dichroism measurements that the selected sequences can indeed adopt G4 conformation in vitro. Analysis of RNA-Seq of polyA RNA in maize seedlings grown in the presence of a G4-stabilizing ligand (NMM) showed both inhibitory as well as stimulatory effects on the transcription of LTR retrotransposons.ConclusionsOur results demonstrate that quadruplex DNA located within long terminal repeats of LTR retrotransposons can be formed in vivo and that it plays a regulatory role in the LTR retrotransposon life-cycle, thus also affecting genome dynamics.
Highlights
Many studies have shown that guanine-rich Deoxyribonucleic acid (DNA) sequences form quadruplex structures (G4) in vitro but there is scarce evidence of guanine quadruplexes in vivo
Selection of maize Long terminal repeat (LTR) retrotransposons with PQS and confirmation of quadruplex formation by circular dichroism We searched for maize LTR retrotransposons having potential quadruplex-forming sequences (PQS) using pqsfinder (Fig. 1; Additional files 3 and 4)
We found that about 37% of all families contained at least one PQS (Fig. 1a) with a tendency to have a higher number of PQS in the same element - on average more than 3 PQS per family
Summary
Many studies have shown that guanine-rich DNA sequences form quadruplex structures (G4) in vitro but there is scarce evidence of guanine quadruplexes in vivo. The majority of potential quadruplex-forming sequences (PQS) are located in transposable elements (TEs), especially close to promoters within long terminal repeats of plant LTR retrotransposons. Many studies have shown that guanine-rich sequences form quadruplex DNA or RNA in vitro but solid experimental evidence of quadruplex formation in vivo has been gathered only recently (for review see [6, 7]) many quadruplexes that are formed in vitro are unfolded in living cells [8]. In the maize genome, mostly composed of LTR retrotransposons, 71% of non-telomeric G4 motifs are located in repetitive genomic regions [5]. Lexa et al [11] analysed 18,377 LTR retrotransposons from 21 plant
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