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.

Basic information

Original name

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

Authors

JEDLIČKA, Pavel (203 Czech Republic, guarantor), Matej LEXA (703 Slovakia, belonging to the institution), Ivan VANÁT (703 Slovakia, belonging to the institution), Eduard KEJNOVSKÝ (203 Czech Republic) and Roman HOBZA (203 Czech Republic)

Edition

Mobile DNA, 2019, 1759-8753

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10611 Plant sciences, botany

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 3.161

RIV identification code

RIV/00216224:14330/19:00114128

Organization unit

Faculty of Informatics

DOI

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

UT WoS

000502731200001

Keywords in English

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

Abstract

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.

Links

GA18-00258S, research and development project

Name: Úloha transposonů v dynamice rostlinných genomů (Acronym: TRANSPOSONY_DRG)

Investor: Czech Science Foundation

Citovat

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. 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.

@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. \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.

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