Additional file 4: of Quadruplex DNA in long terminal repeats in maize LTR retrotransposons inhibits the expression of a reporter gene in yeast

Overview of families, PQS and average lengths. Table S1. Families possessing PQS score > 64. Table S2. Number of PQS score > 64 in superfamilies. Table S3. Average lengths of LTRs, non-LTR regios and whole elements. (XLSX 13 kb

Additional file 2: of Quadruplex DNA in long terminal repeats in maize LTR retrotransposons inhibits the expression of a reporter gene in yeast

Overview of oligonucleotides, BAC clones and primers used in study. Name is derived from Maize TE Database. BAC referes to ZMMBBc library coordinates of clones containing given element. G4 motif coresponds to oligonucleotides used for CD measurments and UV melting. Guanine tracks and mutations are highlighted by bold bigger font in wilde types and mutants respectively. Forward and reverse primers were used for element amplification from BAC clones, the product length is indicated as last colum. Mutagenic primers were used for generating constructs with mutatnt LTRs, mutations are highlighted as mentiond above. RACE and RACE nested primers were used for rapid amlification of cDNA ends in yeast and maize. (XLSX 10 kb

Additional file 5: of Quadruplex DNA in long terminal repeats in maize LTR retrotransposons inhibits the expression of a reporter gene in yeast

CD spectra of oligonucleotides without G4-forming ability. CD spectra of oligonucleotides representing wild-type PQS from various LTR retrotransposons obtained at different concentrations of potassium ions (orange: 0 mM K+; blue: 150 mM K+ and red: 150 mM K+ after annealing). Debeh, Nobe, Hooni, Wuwe and Prem1 are oligonucleotides with long middle loop. Flip has short middle loop. (TIFF 883 kb

Additional file 1: of Quadruplex DNA in long terminal repeats in maize LTR retrotransposons inhibits the expression of a reporter gene in yeast

Annotation of all 579 maize TEs included in this study. The presence and position of detectable LTRs, PBS and PPT sequences (LTR Finder), protein-coding domains (BLASTX) and potential quadruplex sequences (PQS; pqsfinder). White rectangles represent LTRs, blue rectangles are common TE domains (labelled) or other domains detected in Uniprot (unlabelled). Small blue bars are PQS with score > 24 (> 64 larger bar). (PDF 927 kb

Quadruplex-Forming Motif Inserted into 3′UTR of Ty1his3-AI Retrotransposon Inhibits Retrotransposition in Yeast

Guanine quadruplexes (G4s) serve as regulators of replication, recombination and gene expression. G4 motifs have been recently identified in LTR retrotransposons, but their role in the retrotransposon life-cycle is yet to be understood. Therefore, we inserted G4s into the 3′UTR of Ty1his3-AI retrotransposon and measured the frequency of retrotransposition in yeast strains BY4741, Y00509 (without Pif1 helicase) and with G4-stabilization by N-methyl mesoporphyrin IX (NMM) treatment. We evaluated the impact of G4s on mRNA levels by RT-qPCR and products of reverse transcription by Southern blot analysis. We found that the presence of G4 inhibited Ty1his3-AI retrotransposition. The effect was stronger when G4s were on a transcription template strand which leads to reverse transcription interruption. Both NMM and Pif1p deficiency reduced the retrotransposition irrespective of the presence of a G4 motif in the Ty1his3-AI element. Quantity of mRNA and products of reverse transcription did not fully explain the impact of G4s on Ty1his3-AI retrotransposition indicating that G4s probably affect some other steps of the retrotransposon life-cycle (e.g., translation, VLP formation, integration). Our results suggest that G4 DNA conformation can tune the activity of mobile genetic elements that in turn contribute to shaping the eukaryotic genomes