ArticleMobile DNA2019
Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study.
Article in Mobile DNA, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- The pQBR mercury resistance plasmids: a model set of sympatric environmental mobile genetic elements.Microbial genomics · 2026Article
- Factors determining chromosomal localization of transposable elements in plants.Plant biology (Stuttgart, Germany) · 2025Review
- Retand LTR-retrotransposons in plants: a long way from pol to 3'LTR.Mobile DNA · 2025Article
- PTGS is dispensable for the initiation of epigenetic silencing of an active transposon in Arabidopsis.EMBO reports · 2024Article
- Sexy ways: approaches to studying plant sex chromosomes.Journal of experimental botany · 2024Review
- Noncanonical DNA structures are drivers of genome evolution.Trends in genetics : TIG · 2023Review
- Amplification of LTRs of extrachromosomal linear DNAs (ALE-seq) identifies two active Oryco LTR retrotransposons in the rice cultivar Dongjin.Mobile DNA · 2022Article
- Review
- Retrotransposons: How the continuous evolutionary front shapes plant genomes for response to heat stress.Frontiers in plant science · 2022Review
- The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation.International journal of molecular sciences · 2021Review
- Rapid Genome Evolution and Adaptation ofFrontiers in plant science · 2021Article
- Mobility connects: transposable elements wire new transcriptional networks by transferring transcription factor binding motifs.Biochemical Society transactions · 2020Review
- Article
Corrections and comments
- Erratum issued
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNesting is common in LTR retrotransposons, especially in large genomes containing a high number of elements.
resultsWe 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.
conclusionsWe 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.
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