A Snapshot of Histone Modifications within Transposable Elements in Drosophila Wild Type Strains

Rita Rebollo,Flora Begeot,Cristina Vieira,Marion Delattre,Eric Gilson,Béatrice Horard,Nadia Singh

doi:10.1371/journal.pone.0044253

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.

Highlights

Transposable elements (TEs) are a major source of genetic novelty and genome evolution [1,2]
In order to study the chromatin environment of different transposable elements in several wild type strains of both D. melanogaster and D. simulans, we performed cross-linked chromatin immunoprecipitation (X-CHIP) with antibodies specific for euchromatin (H3K4me2), facultative heterochromatin (H3K27me3) and constitutive heterochromatin (H3K9me2) in two to four biological replicates of late embryos for seven wild type strains of Drosophila
F copies are consistently associated with heterochromatic marks in D. melanogaster and in D. simulans (Figure 2). 412 elements harbor no distinct pattern of histone modifications and some strains lack all histones modifications assayed

Summary

Introduction

Transposable elements (TEs) are a major source of genetic novelty and genome evolution [1,2]. The factors that govern intra- and inter-species TE diversity are complex They consist of a combination of the intrinsic properties of the TEs themselves (e.g. transposition mechanism, infectivity), the properties of the host’s ecology (e.g. effective size and structure of the populations), and those of the genome (e.g. TE regulation, gene density, genome size). H3K4me is observed along with the previous repressive marks, in both promoter and ORF of the HET-A LTR retrotransposon [19] Association of both repressive (H3K9me2/ 3) and permissive (H3K4me2/3) histone marks was observed in retrotransposons found in both euchromatin and heterochromatin regions, the enrichment for H3K4me2/3 is weak or moderate in the latter [20,21]. The histone modifications associated with TEs in Drosophila are still poorly understood, and are rarely discussed in the literature

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Results

Conclusion