Quadruplex-forming sequences occupy discrete regions inside plant LTR retrotransposons

0440128 - BFÚ 2015 RIV GB eng J - Journal Article
Lexa, M. - Kejnovský, Eduard - Šteflová, Pavlína - Konvalinová, H. - Vorlíčková, Michaela - Vyskot, Boris
Quadruplex-forming sequences occupy discrete regions inside plant LTR retrotransposons.
Nucleic Acids Research. Roč. 42, č. 2 (2014), s. 968-978. ISSN 0305-1048. E-ISSN 1362-4962
R&D Projects: GA ČR(CZ) GAP205/12/0466; GA ČR(CZ) GAP305/10/0930; GA ČR(CZ) GAP501/10/0102; GA ČR(CZ) GA522/09/0083; GA ČR GPP501/10/P483
Institutional support: RVO:68081707
Keywords : INTRAMOLECULAR DNA QUADRUPLEXES * VIRUS TYPE-1 RNA * CIRCULAR-DICHROISM
Subject RIV: BO - Biophysics
Impact factor: 9.112, year: 2014

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.
Permanent Link: http://hdl.handle.net/11104/0243250