Sensitive detection of pre-integration intermediates of long terminal repeat retrotransposons in crop plants
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Sensitive detection of pre-integration intermediates of long terminal repeat retrotransposons in crop plants. / Cho, Jungnam; Benoit, Matthias; Catoni, Marco; Drost, Hajk-Georg; Brestovitsky, Anna; Oosterbeek, Matthijs; Paszkowski, Jerzy.
In: Nature Plants, Vol. 5, 01.01.2019, p. 26-33.Research output: Contribution to journal › Letter › peer-review
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TY - JOUR
T1 - Sensitive detection of pre-integration intermediates of long terminal repeat retrotransposons in crop plants
AU - Cho, Jungnam
AU - Benoit, Matthias
AU - Catoni, Marco
AU - Drost, Hajk-Georg
AU - Brestovitsky, Anna
AU - Oosterbeek, Matthijs
AU - Paszkowski, Jerzy
PY - 2019/1/1
Y1 - 2019/1/1
N2 - Retrotransposons have played an important role in the evolution of host genomes1,2. Their impact is mainly deduced from the composition of DNA sequences that have been fixed over evolutionary time2. 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 Arabidopsis3. However, SIRT cannot be applied to large and transposon-rich 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. ALE-seq 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 eclDNAs 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.
AB - Retrotransposons have played an important role in the evolution of host genomes1,2. Their impact is mainly deduced from the composition of DNA sequences that have been fixed over evolutionary time2. 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 Arabidopsis3. However, SIRT cannot be applied to large and transposon-rich 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. ALE-seq 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 eclDNAs 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.
KW - Arabidopsis/genetics
KW - Computational Biology/methods
KW - Crops, Agricultural/genetics
KW - Gene Expression Regulation, Plant
KW - Heat-Shock Response/genetics
KW - Lycopersicon esculentum/genetics
KW - Oryza/genetics
KW - Retroelements/genetics
KW - Sequence Analysis, DNA/methods
KW - Terminal Repeat Sequences
UR - http://www.scopus.com/inward/record.url?scp=85058144653&partnerID=8YFLogxK
U2 - 10.1038/s41477-018-0320-9
DO - 10.1038/s41477-018-0320-9
M3 - Letter
C2 - 30531940
VL - 5
SP - 26
EP - 33
JO - Nature Plants
JF - Nature Plants
SN - 2055-026X
ER -