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Review
. 2020 Jul 3:11:23.
doi: 10.1186/s13100-020-00213-z. eCollection 2020.

Transposable elements in Drosophila

Vincent Mérel  1 , Matthieu Boulesteix  1 , Marie Fablet  1 , Cristina Vieira  1
Affiliations
Review

Transposable elements in Drosophila

Vincent Mérel et al. Mob DNA. .

Abstract

Drosophila has been studied as a biological model for many years and many discoveries in biology rely on this species. Research on transposable elements (TEs) is not an exception. Drosophila has contributed significantly to our knowledge on the mechanisms of transposition and their regulation, but above all, it was one of the first organisms on which genetic and genomic studies of populations were done. In this review article, in a very broad way, we will approach the TEs of Drosophila with a historical hindsight as well as recent discoveries in the field.

Keywords: Drosophila; Population genomics; epigenetics; intra and interspecific TE diversity.

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Conflict of interest statement

Competing interestsThe authors declare that they have no competing interests

Figures

Fig. 1
Fig. 1
TE structure and transposition mechanisms. LTR retrotransposons: 1. Transcription. 2. Translation of one part of the transcripts. The protease (Prot) cleaves pol polyprotein. 3. gag proteins assemble around untranslated transcripts, the integrase (Int), reverse transcriptase (RT) and a tRNA. 4. Reverse transcription and integration. LINE retrotransposons: 1. Transcription. 2. Translation. 3. Protein(s) bind to the transcript. 4. A strand of donor DNA is cut, target-primed reverse transcription starts at the exposed 3’ extremity. 5. The TE is integrated. TIR DNA transposons: 1. Transcription. 2. Translation. 3. Two transposases bind to the TIRs. 4. Transposases dimerize and cut TIR extremities forming a free complex. 5. The complex binds to donor DNA and is integrated. Helitron DNA transposons: 1. Transcription. 2. Translation. 3. At the donor site, the plus strand is cut. A replication fork is formed. 4. Replication results in a double stranded transposon circle. 5. Integration. The bottom right panel represents the distribution of the lengths of D. melanogaster consensus sequences (RepBase [56]), using the same color code as above.
Fig. 2
Fig. 2
TE contents in D. melanogaster, D. simulans and D. virilis (from left to right). Barplots represent TE copy numbers for the top 20 TE superfamilies. Piecharts illustrate genomic sequence occupancy of each TE order (in percentages of the assemblies). These results were obtained using the D. melanogaster reference genome assembly (r6.29), and recently produced long-reads assemblies of D. simulans and D. virilis [99]. RepeatMasker was used to recover TE fragments and TE genomic sequence occupancy (RepeatMasker v1.332, -nolow, -norna, -species drosophila; Repbase-derived RepeatMasker libraries 20181026 [100],). TE fragments were assembled into TE copies using OneCodeToFindThemAll [101].
Fig. 3
Fig. 3
TE landscapes in D. melanogaster and D. simulans. For each TE fragment the divergence to consensus was estimated. For each TE order the total amount of DNA (in bp) is shown as a function of the percentage of divergence. The percentage of divergence to the consensus sequences is a proxy for age: old TEs have accumulated mutations, young TEs are similar to consensus sequences. RepeatMasker was used to recover TE fragments in genomic assemblies (same method as Figure 2 [100],). Percentages of divergence to consensus were evaluated from RepeatMasker output .align file using A. Kapusta script [154]
Fig. 4
Fig. 4
small RNA pathways controlling TEs. piRNA pathway: 1. RNA PolII transcribes a genomic piRNA cluster into a long single stranded RNA. 2. The transcript thus formed enters the ping-pong pathway, which is ensured by Aub and Ago3, generates sense and antisense piRNAs, and ensure post-transcriptional silencing by transcript slicing. 3. Piwi directs the cleavage of the piRNA cluster transcript and generates a piRNA. This step may be repeated. 4. Transcriptional silencing: in the nucleus, a piRNA guides Piwi and promotes H3K9 methylation of TE DNA sequences. siRNA pathway: 1. Generation of a long dsRNA by: a. bi-directional transcription of a unique TE locus, b. interaction of two complementary transcripts from distinct TE loci. c. hairpin formation, due for example to inverted repeats binding 2. Dcr-2 processes long dsRNAs into siRNAs, which are loaded on Ago2. 3. The passenger strand of the siRNA is sliced by Ago2, only the guide strand remains. 4. The RISC binds to a TE transcript with sequence complementarity to the guide strand and Ago2 cleaves it.
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