A snapshot of histone modifications within transposable elements in Drosophila wild type strains

Abstract

Transposable elements (TEs) are a major source of genetic variability in genomes, creating genetic novelty and driving genome evolution. Analysis of sequenced genomes has revealed considerable diversity in TE families, copy number, and localization between different, closely related species. For instance, although the twin species Drosophila melanogaster and D. simulans share the same TE families, they display different amounts of TEs. Furthermore, previous analyses of wild type derived strains of D. simulans have revealed high polymorphism regarding TE copy number within this species. Several factors may influence the diversity and abundance of TEs in a genome, including molecular mechanisms such as epigenetic factors, which could be a source of variation in TE success. In this paper, we present the first analysis of the epigenetic status of four TE families (roo, tirant, 412 and F) in seven wild type strains of D. melanogaster and D. simulans. Our data shows intra- and inter-specific variations in the histone marks that adorn TE copies. Our results demonstrate that the chromatin state of common TEs varies among TE families, between closely related species and also between wild type strains.

Figure 1. Cartoon of the four retrotransposons studied (not to scale).

Colored boxes represent open reading frames (ORF) and white boxes long terminal repeats (LTR). Arrows represent the quantitative PCR primers used for ChIP-qPCR (black arrows) and expression analysis (red arrows). The size of each canonical element is given.

Figure 2. Histone post-translational modifications associated with Drosophila transposable elements.

Heatmap of ChIP-qPCR average fold enrichment for all TEs analyzed. Fold enrichment for each wild type strain is normalized by input, hence copy number, and also by actin, allowing comparison of species and srains. Each row represents a wild type strain of either D. melanogaster (DM) or D. simulans (DS). Each column represents a different antibody used (H3K4me2, H3K27me3 and H3K9me2). Location of primers used for ChIP-qPCR amplification is shown in Figure 1.

Figure 3. D. melanogaster and D. simulans display differences in TE chromatin state and expression of epigenetic writers.

A. Fold enrichment of H3K9me2 (left panel) and H3K27me3 (right panel) for the four transposable elements studied are depicted per species (mean ± SE). Roo copies show a significant lack of H3K9me2 (Mann Whitney test, p-value <0.05). Histone fold enrichment of each TE family was compared between species and the results of the Mann Whitney test are shown (p-value * <0.05 and Δ <0.1). B. Quantification of RNA steady-state levels of the methyltransferases responsible for H3K9me2 and H3K27me3 deposition (mean ± SE). D. melanogaster (blue), D. simulans (red). Mann Whitney P-values between species are shown with asterisks (p-value ** <0.001).

Figure 4. Expression of transposable element families in D. melanogaster (blue) and D. simulans (red).

Mann Whitney P-values are shown with asterisks (p-value *<0.05).