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

0520376 - BFÚ 2020 RIV GB eng J - Journal Article
Jedlička, Pavel - Lexa, M. - Vanat, I. - Hobza, Roman - Kejnovský, Eduard
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. Roč. 10, č. 1 (2019), č. článku 50. ISSN 1759-8753. E-ISSN 1759-8753
R&D Projects: GA ČR(CZ) GA18-00258S; GA ČR GA16-08698S
Institutional support: RVO:68081707
Keywords : insertion site preferences * transposable elements * molecular-biology * genome structure * dna segments
OECD category: Genetics and heredity (medical genetics to be 3)
Impact factor: 3.161, year: 2019
Method of publishing: Open access
https://mobilednajournal.biomedcentral.com/track/pdf/10.1186/s13100-019-0186-z

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 a low negative impact on family fitness supports the concept of the genome being viewed as an ecosystem of various elements.
Permanent Link: http://hdl.handle.net/11104/0305055