Nested plant LTR retrotransposons target specific regions of
other elements, while all LTR retrotransposons often target
palindromes and nucleosome-occupied regions: in silico study

J 2019

Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study

JEDLIČKA, Pavel, Matej LEXA, Ivan VANÁT, Eduard KEJNOVSKÝ, Roman HOBZA et. al.

Základní údaje

Originální název

Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study

Autoři

JEDLIČKA, Pavel (203 Česká republika, garant), Matej LEXA (703 Slovensko, domácí), Ivan VANÁT (703 Slovensko, domácí), Eduard KEJNOVSKÝ (203 Česká republika) a Roman HOBZA (203 Česká republika)

Vydání

Mobile DNA, 2019, 1759-8753

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10611 Plant sciences, botany

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 3.161

Kód RIV

RIV/00216224:14330/19:00114128

Organizační jednotka

Fakulta informatiky

DOI

http://dx.doi.org/10.1186/s13100-019-0186-z

UT WoS

000502731200001

Klíčová slova anglicky

Transposable elements; LTR retrotransposons; Nesting; Chromatin; Nucleosomes; Plants

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 6. 5. 2020 17:12, RNDr. Pavel Šmerk, Ph.D.

Anotace

V originále

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.

Návaznosti

GA18-00258S, projekt VaV

Název: Úloha transposonů v dynamice rostlinných genomů (Akronym: TRANSPOSONY_DRG)

Investor: Grantová agentura ČR, Úloha transposonů v dynamice rostlinných genomů

Citovat

JEDLIČKA, Pavel, Matej LEXA, Ivan VANÁT, Eduard KEJNOVSKÝ a 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. Mobile DNA. 2019, roč. 10, č. 1, s. 1-14. ISSN 1759-8753. Dostupné z: https://dx.doi.org/10.1186/s13100-019-0186-z.

@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 a 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. \textit{Mobile DNA}. 2019, roč.~10, č.~1, s.~1-14. ISSN~1759-8753. Dostupné z: https://dx.doi.org/10.1186/s13100-019-0186-z.

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