Quadruplex-forming sequences occupy discrete regions inside plant LTR retrotransposons

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.

Conformational diversity of single‐stranded DNA from bacterial repetitive extragenic palindromes: Implications for the DNA recognition elements of transposases

“…Bioinformatic evidence has provided insight into sequence diversity and categories of G-tetraplex-forming sequences in intronic regions of the human genome 58 and their sequence, topology, and structural properties have been reviewed 59. Such structures also are enriched upstream and within gene promoters, which can lead to inhibition of transcription initiation,60 and may regulate retro-transposition in plants 61. G-tetraplex structures have become a promising target of anticancer drugs,62 which suggests that tetraplex prone REP elements represent potential drug targets as well.…”

“…59 Such structures also are enriched upstream and within gene promoters, which can lead to inhibition of transcription initiation, 60 and may regulate retro-transposition in plants. 61 G-tetraplex structures have become a promising target of anticancer drugs, 62 which suggests that tetraplex prone REP elements represent potential drug targets as well.…”

Two-Quartet G-Quadruplexes Formed by DNA Sequences Containing Four Contiguous GG Runs

“…[21][22] As a result, these G-quadruplexes with various loop lengths are stable under physiological conditions. 21, [23][24][25][26][27] Theoretically, the sequence containing four contiguous runs of two guanine bases (G 2 N x G 2 N y G 2 N z G 2 , G 2 sequence) has the potential to fold into two quartets, forming a two-quartet G-quadruplex. Additionally, there are reports about such G-quadruplex structures formed by telomere DNAs and DNA aptamers.…”

Structure, properties, and biological relevance of the DNA and RNA G-quadruplexes: Overview 50 years after their discovery

“…They are distributed non ran domly primarily away from the regions involved in nucle osome formation and in non methylated regions [65]. High frequency of G4 motifs is observed within telomer ic DNA [66] and micro(mini)satellite repeats [67,68], in long terminal repeats (LTRs) of retrotransposons [69], in genes of ribosomal RNA, in regulatory regions of the genome such as gene promoters [70]; predominately in the coding (sense) strand [71], in origins of replication [5,72,73], in immunoglobulin switch regions and break point regions of chromosome translocation [74], recom bination hotspots [75], intronic sequences [76,77], CpG islands, enhancers, and insulators [78], in mitochondrial DNA [79], as well as in various regions of the transcrip tome including sites of alternative mRNA processing, splicing [80], 5′ and 3′ untranslated mRNA regions [2], telomeric non coding RNA [81], pre microRNA [82], and long non coding RNA [83].…”

“…In plants, quadruplex forming sequences acting as translation repressors were found in 5′ untranslated regions (UTR) of mRNA [91]. Retrotransposon LTRs, which are highly abundant in plants, contain a large number of G4 motifs [69].…”