Sensitive detection of pre-integration intermediates of LTR retrotransposons in crop plants - Archive ouverte HAL Accéder directement au contenu
Article Dans Une Revue Nature Plants Année : 2019

Sensitive detection of pre-integration intermediates of LTR retrotransposons in crop plants

Résumé

Retrotransposons have played an important role in the evolution of host genomes 1,2. Their impact is mainly deduced from the composition of DNA sequences that have been fixed over evolutionary time 2. Such studies provide important 'snapshots' reflecting the historical activities of transposons but do not predict current transposition potential. We previously reported sequence-independent retrotransposon trapping (SIRT) as a method that, by identification of extrachromosomal linear DNA (eclDNA), revealed the presence of active long terminal repeat (LTR) retrotransposons in Arabidopsis 3. However, SIRT cannot be applied to large and transposonrich genomes, as found in crop plants. We have developed an alternative approach named ALE-seq (amplification of LTR of eclDNAs followed by sequencing) for such situations. ALEseq reveals sequences of 5′ LTRs of eclDNAs after two-step amplification: in vitro transcription and subsequent reverse transcription. Using ALE-seq in rice, we detected eclD-NAs for a novel Copia family LTR retrotransposon, Go-on, which is activated by heat stress. Sequencing of rice accessions revealed that Go-on has preferentially accumulated in Oryza sativa ssp. indica rice grown at higher temperatures. Furthermore, ALE-seq applied to tomato fruits identified a developmentally regulated Gypsy family of retrotransposons. A bioinformatic pipeline adapted for ALE-seq data analyses is used for the direct and reference-free annotation of new, active retroelements. This pipeline allows assessment of LTR retrotransposon activities in organisms for which genomic sequences and/or reference genomes are either unavailable or of low quality. Chromosomal copies of activated retrotransposons containing LTRs are transcribed by RNA polymerase II, followed by reverse transcription of transcripts to eclDNA; these integrate back into host chromosomes 3. Because of the two obligatory template switches during reverse transcription, the newly synthetized eclDNA is flanked by LTRs of identical sequence. Their subsequent divergence due to the accumulation of mutations correlates well with length of time since the last transposition and thus transposon age 4. However, the age of LTR retrotransposons cannot be used to predict their current transpositional potential. Predictions are further complicated by recombination events that occur with high frequency between young and old members of a retrotransposon family 5 ; old family
Fichier principal
Vignette du fichier
317479v1.full.pdf (1.04 Mo) Télécharger le fichier
Origine : Fichiers produits par l'(les) auteur(s)

Dates et versions

hal-04171191 , version 1 (22-08-2023)

Identifiants

Citer

Jungnam Cho, Matthias Benoit, Marco Catoni, Hajk-Georg Drost, Anna Brestovitsky, et al.. Sensitive detection of pre-integration intermediates of LTR retrotransposons in crop plants. Nature Plants, 2019, 5 (1), pp.26-33. ⟨10.1038/s41477-018-0320-9⟩. ⟨hal-04171191⟩
1 Consultations
8 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More