Whereas facultative heterochromatin is preferentially labeled by H3K27me3. While studying the heterochromatin-euchromatin boundary, Yasuhara et al. showed that TEs are associated with H3K9me2 in D. melanogaster embryos and high copy number TEs, such as the LTR retrotransposon roo, have lower H3K9me2 enrichment. In Drosophila somatic tissues different retrotransposons are associated with H3K9me3 and H3K9me2 in both their promoter regions and open reading frames. Interestingly, H3K4me2 is observed along with the previous repressive marks, in both promoter and ORF of the HET-A LTR retrotransposon. Association of both repressive and permissive histone marks was also observed in retrotransposons found in both euchromatin and heterochromatin regions, although the enrichment for H3K4me2/3 is weak or moderate in the latter. In addition to the complex association of histone marks and TEs observed in Drosophila, there is evidence that distinct chromatin patterns might be observed not only between different TE families as noted above, but also within a given TE family. Therefore, the histone modifications associated with TEs in Drosophila are still poorly understood, and are rarely discussed in the literature. Drosophila has fewer TEs than other organisms, such as humans;15% of the Drosophila genome is composed by TEs versus 50% for humans ; but has a high level of TE activity, as demonstrated by the large number of spontaneous mutations that are attributed to TE movements, and by the high number of fulllength TEs found in the sequenced genome of D. melanogaster. Drosophila contains putative active elements, and hence is an interesting model for studying the impact of TEs on genetic variability and genome evolution. D. melanogaster and D. simulans contain the same TE families, with more than 90% of sequence identity in most cases. However, an over-representation of almost all TEs is observed in D. melanogaster, as shown by the sequenced genome analysis of both species. This study estimates that euchromatic TEs account for,5% and 2% of the genome in D. melanogaster and D. simulans respectively. Investigation of TEs and associated histone modifications has never been carried out in a natural population of Drosophila. This restricts our understanding of the mechanisms that control TE behavior and dynamics in genomes to a static view. Wild type derived strains of natural populations of both D. melanogaster and D. simulans provide an excellent model system to investigate these questions. Such strains have been collected from different geographic locations in the last 30 years and have been maintained as inbred lines in the laboratory. Copy WY 14643 numbers of TEs are relatively homogeneous in wild type strains of D. melanogaster, since high numbers of copies are present in all the strains analyzed. In contrast, wild type strains of D. simulans are highly variable; a high copy number of a given element may be observed in one strain, with no copies in another strain. These observations were based on counting the TE copy number through polytene chromosome in-situ hybridization experiments in which TEs of centromeric, telomeric and dense heterochromatic regions cannot be counted individually. Therefore, the variations in copy number observed between wild type strains of D. melanogaster and D. simulans reflect only euchromatic copies. Such differences suggest different levels of TE regulation or population biology in both species.