Cargando…
Quadruplex-forming sequences occupy discrete regions inside plant LTR retrotransposons
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)...
Autores principales: | , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2014
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3902901/ https://www.ncbi.nlm.nih.gov/pubmed/24106085 http://dx.doi.org/10.1093/nar/gkt893 |
_version_ | 1782301040771596288 |
---|---|
author | Lexa, Matej Kejnovský, Eduard Šteflová, Pavlína Konvalinová, Helena Vorlíčková, Michaela Vyskot, Boris |
author_facet | Lexa, Matej Kejnovský, Eduard Šteflová, Pavlína Konvalinová, Helena Vorlíčková, Michaela Vyskot, Boris |
author_sort | Lexa, Matej |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-3902901 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-39029012014-01-27 Quadruplex-forming sequences occupy discrete regions inside plant LTR retrotransposons Lexa, Matej Kejnovský, Eduard Šteflová, Pavlína Konvalinová, Helena Vorlíčková, Michaela Vyskot, Boris Nucleic Acids Res Genomics 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. Oxford University Press 2014-01 2013-10-06 /pmc/articles/PMC3902901/ /pubmed/24106085 http://dx.doi.org/10.1093/nar/gkt893 Text en © The Author(s) 2013. Published by Oxford University Press. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Genomics Lexa, Matej Kejnovský, Eduard Šteflová, Pavlína Konvalinová, Helena Vorlíčková, Michaela Vyskot, Boris Quadruplex-forming sequences occupy discrete regions inside plant LTR retrotransposons |
title | Quadruplex-forming sequences occupy discrete regions inside plant LTR retrotransposons |
title_full | Quadruplex-forming sequences occupy discrete regions inside plant LTR retrotransposons |
title_fullStr | Quadruplex-forming sequences occupy discrete regions inside plant LTR retrotransposons |
title_full_unstemmed | Quadruplex-forming sequences occupy discrete regions inside plant LTR retrotransposons |
title_short | Quadruplex-forming sequences occupy discrete regions inside plant LTR retrotransposons |
title_sort | quadruplex-forming sequences occupy discrete regions inside plant ltr retrotransposons |
topic | Genomics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3902901/ https://www.ncbi.nlm.nih.gov/pubmed/24106085 http://dx.doi.org/10.1093/nar/gkt893 |
work_keys_str_mv | AT lexamatej quadruplexformingsequencesoccupydiscreteregionsinsideplantltrretrotransposons AT kejnovskyeduard quadruplexformingsequencesoccupydiscreteregionsinsideplantltrretrotransposons AT steflovapavlina quadruplexformingsequencesoccupydiscreteregionsinsideplantltrretrotransposons AT konvalinovahelena quadruplexformingsequencesoccupydiscreteregionsinsideplantltrretrotransposons AT vorlickovamichaela quadruplexformingsequencesoccupydiscreteregionsinsideplantltrretrotransposons AT vyskotboris quadruplexformingsequencesoccupydiscreteregionsinsideplantltrretrotransposons |