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

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14330%2F19%3A00114128" target="_blank" >RIV/00216224:14330/19:00114128 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/68081707:_____/19:00520376

Výsledek na webu

<a href="https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-019-0186-z" target="_blank" >https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-019-0186-z</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1186/s13100-019-0186-z" target="_blank" >10.1186/s13100-019-0186-z</a>

Jazyk výsledku

angličtina

Název v původním jazyce

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

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

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

Popis výsledku anglicky

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.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10611 - Plant sciences, botany

Projekt

<a href="/cs/project/GA18-00258S" target="_blank" >GA18-00258S: Úloha transposonů v dynamice rostlinných genomů</a><br>

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2019

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Mobile DNA

ISSN

1759-8753

e-ISSN

—

Svazek periodika

10

Číslo periodika v rámci svazku

1

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

14

Strana od-do

1-14

Kód UT WoS článku

000502731200001

EID výsledku v databázi Scopus

2-s2.0-85076528441