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@article{1652716,
author = {Jedlička, Pavel and Lexa, Matej and Vanát, Ivan and Kejnovský, Eduard and Hobza, Roman},
article_number = {1},
doi = {http://dx.doi.org/10.1186/s13100-019-0186-z},
keywords = {Transposable elements; LTR retrotransposons; Nesting; Chromatin; Nucleosomes; Plants},
language = {eng},
issn = {1759-8753},
journal = {Mobile DNA},
title = {Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study},
url = {https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-019-0186-z},
volume = {10},
year = {2019}
}
TY - JOUR
ID - 1652716
AU - Jedlička, Pavel - Lexa, Matej - Vanát, Ivan - Kejnovský, Eduard - Hobza, Roman
PY - 2019
TI - Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study
JF - Mobile DNA
VL - 10
IS - 1
SP - 1-14
EP - 1-14
SN - 17598753
KW - Transposable elements
KW - LTR retrotransposons
KW - Nesting
KW - Chromatin
KW - Nucleosomes
KW - Plants
UR - https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-019-0186-z
L2 - https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-019-0186-z
N2 - Background:Nesting is common in LTR retrotransposons, especially in large genomes containing a high number of elements.Results:We analyzed 12 plant genomes and obtained 1491 pairs of nested and original (pre-existing) LTR retrotransposons. We systematically analyzed mutual nesting of individual LTR retrotransposons and found that certain families, more often belonging to the Ty3/gypsy than Ty1/copia superfamilies, showed a higher nesting frequency as well as a higher preference for older copies of the same family (“autoinsertions”). Nested LTR retrotransposons were preferentially located in the 3’UTR of other LTR retrotransposons, while coding and regulatory regions (LTRs) are not commonly targeted. Insertions displayed a weak preference for palindromes and were associated with a strong positional pattern of higher predicted nucleosome occupancy. Deviation from randomness in target site choice was also found in 13,983 non-nested plant LTR retrotransposons.Conclusions:We reveal that nesting of LTR retrotransposons is not random. Integration is correlated with sequence composition, secondary structure and the chromatin environment. Insertion into retrotransposon positions with allow negative impact on family fitness supports the concept of the genome being viewed as an ecosystem of various elements.
ER -
JEDLIČKA, Pavel, Matej LEXA, Ivan VANÁT, Eduard KEJNOVSKÝ and Roman HOBZA. Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study. Online. \textit{Mobile DNA}. 2019, vol.~10, No~1, p.~1-14. ISSN~1759-8753. Available from: https://dx.doi.org/10.1186/s13100-019-0186-z. [citováno 2024-04-24]
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