Abstract
Retrotransposons with long terminal repeats (LTR) form a significant proportion of eukaryotic genomes, especially in plants. They have gag and pol genes and several regulatory regions necessary for transcription and reverse transcription. We searched for potential quadruplex-forming sequences (PQSs) and potential triplex-forming sequences (PTSs) in 18 377 full-length LTR retrotransposons collected from 21 plant species. We found that PQSs were often located in LTRs, both upstream and downstream of promoters from which the whole retrotransposon is transcribed. Upstream-located guanine PQSs were dominant in the minus DNA strand, whereas downstream-located guanine PQSs prevailed in the plus strand, indicating their role both at transcriptional and post-transcriptional levels. Our circular dichroism spectroscopy measurements confirmed that these PQSs readily adopted guanine quadruplex structures—some of them were paralell-stranded, while others were anti-parallel-stranded. The PQS often formed doublets at a mutual distance of up to 400 bp. PTSs were most abundant in 3′UTR (but were also present in 5′UTR). We discuss the potential role of quadruplexes and triplexes as the regulators of various processes participating in LTR retrotransposon life cycle and as potential recombination sites during post-insertional retrotransposon-based genome rearrangements.
Highlights
Transposable elements form a significant proportion of eukaryotic genomes, representing $50% of the human genome and up to 90% of genomes in some plant species
We found that PQS3 present in plus strand (PQS3+) were frequently localized in the 30 half of both left and right long terminal repeats (LTR) (Figure 1a and Supplementary Figure S1)
The peak corresponding to the PQS3À was high in the left LTR, whereas it was blurred in the right LTR, partly because of different relative beginnings of the right LTRs (Figure 1b)
Summary
Transposable elements form a significant proportion of eukaryotic genomes, representing $50% of the human genome and up to 90% of genomes in some plant species. Long terminal repeat (LTR) retrotransposons that are especially common in plants have a duplicative mode of spreading via RNA intermediate and contain gag and pol genes [for a review, see [1]]. Retroviruses and some LTR retrotransposons have an env gene, which is necessary for their virulence. In addition to their genes, LTR retrotransposons have many regulatory sequences, such as LTRs containing promoters where transcription of the whole element starts, primer-binding site (PBS) and polypurine tract (PPT) where reverse transcription of the first and the second strands, respectively, starts [2]. Psi element is a structural feature composed of four stem loop sequences called SL1 to SL4 [4]. Stem loop sequences are characterized by the formation of hairpin structures indicating that secondary DNA structures are functionally involved in the retrovirus life cycle
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
