Levels of DNA cytosine methylation in the Drosophila genome

Introduction

The epigenome of an organism constitutes histone modifications (Zentner & Henikoff, 2013), non-coding RNA molecules (Busto et al., 2015; Stuwe, Tóth & Aravin, 2014) and nucleotide modifications (Achwal, Ganguly & Chandra, 1984; Achwal, Iyer & Chandra, 1983; Gowher, Leismann & Jeltsch, 2000; Zhang et al., 2015). These modifications can together or independently influence the regulation of gene expression and conserve the energy resources by managing functional conformation of the genome (Zee et al., 2016). The epigenetic changes are important in the insect taxon which commonly exhibits polyphenisms (Simpson, Sword & Lo, 2011). Unlike mammals and plants, the sparse methylation of gene bodies and transposons is characteristic of insect DNA methylation (Li-Byarlay, 2016). In social insects with the canonical DNMT1 and DNMT3A/3B methyltransferases, DNA methylation can be attributed to differential splicing, regulation of expression and histone occupancy, whereas very little is known in solitary insects which mostly possess only DNMT2 methyltransferase (Glastad, Hunt & Goodisman, 2014).

The members of genus Drosophila undergo holometabolous development beginning with the embryonic stage which eventually develops into an adult fly after passing through larval and pupal stages (Hartenstein, 1993). There are various changes observed in the DNA methylation patterns of model systems like the house mouse during their development from embryo to adulthood (Smith et al., 2012; Smith & Meissner, 2013). Some previous studies report the presence of low levels of 5-methylcytosine (5mC) and an active DNA methyltransferase in Drosophila melanogaster (Achwal, Ganguly & Chandra, 1984; Achwal, Iyer & Chandra, 1983; Gowher, Leismann & Jeltsch, 2000; Panikar et al., 2015). Recently, the presence of 5mC (less than 1%) in D. melanogaster genome was confirmed by 5mC-specific immunoprecipitation followed by bisulfite sequencing in stage 5 embryos (Takayama et al., 2014) and liquid chromatography/tandem mass spectrometry in adult stage (Capuano et al., 2014; Rasmussen et al., 2016). Bisulphite sequencing is a commonly used method for detection of genome-wide DNA methylation as it provides sequence context information of methylated cytosine residues. However, this method has limitations due to the lower concentration range, incomplete bisulphite conversion of unmethylated cytosines and misalignment of sequenced reads due to genomic repeats, telomeres and GC-rich regions (Warnecke et al., 2002). Using an alternative LCMS-based protocol, Capuano et al., 2014 have reported DNA methylation over a large range from 0.034% of cytosines methylated in a sample with females and males in equal proportion of wt/w118 D. melanogaster adults to 7.6% in liver tissue from Mus musculus and 14% from leaf tissue of Arabidopsis thaliana. The level of DNA methylation in Drosophila is 10–100 folds below the detection limit of bisulphite sequencing. This study established the advantage of an LCMS-based method to assess the levels of DNA methylation in systems like Drosophila with low levels of 5mC.

It is known that DNA methylation patterns change due to the life cycle stage, the tissue or cell type and the age of the specimen under consideration (Lokk et al., 2014). Independent studies mentioned above have demonstrated the presence of 5mC by different techniques in the embryo and adult stages of D. melanogaster. We have estimated the amount of 5mC in the genome of D. melanogaster (across all the life cycle stages) and other 11 species from genus Drosophila using ultra-high performance liquid chromatography/triple quadrupole mass spectrometry. Our analysis determines the change in the levels of 5mC during holometabolous development within a species and also between member species of genus Drosophila.

Materials & Methods

Results

In order to analyse the presence of DNA methylation in the members of genus Drosophila we first standardised the protocol for detection of 5mC detection in D. melanogaster using the UHPLC/QQQ.

The comparison of samples from the life cycle stages of D. melanogaster by Kruskal-Wallis (KW) test shows a significant difference between the levels of 5mC (KW, p = 0.001). The late stages of the embryo in our study represent the stages of development after cellularization and the germ band elongation has been completed. The embryonic stages from 12 to 16 used for representing the late embryos maintain the same general body plan across the later stages in the life cycle. These embryonic stages exhibit significantly high levels of 5mC amongst all the life cycle stages of D. melanogaster.

Also, there is a significant difference between DNA methylation of the third instar larva and both sexes of the adult stage (MW, p = 0.04). The ratio of %5mdC/dC does not show statistically significant difference amongst other stages in the life cycle (Fig. 1A) (Table 1, Supplementary File). There is a decrease in the levels of 5mC after metamorphic transition following the larval stage which is maintained throughout development. The early pupae or white pupae, the sexually distinct pupal and adult stages show similar levels of global DNA methylation. This indicates that there is no sex-specific difference in the levels of 5mC in age-matched samples of the same stage.

Using a combination of the current D. melanogaster genome release by FlyBase and our results with a Perl script to count the number of deoxyribonucleotides in the genome, we have extrapolated the number of modified cytosines in each developmental stage (details in Supplementary File, sheet 2). The number of methylated cytosines per copy of genome in each developmental stage and nucleotide composition of the fly genome are represented in (Fig. 1B).

Although the overall levels remain comparable, the changes in the local patterns of DNA cytosine methylation cannot be ruled out. The head tissue distinctly has a higher level of 5mC when compared to the whole body of the adult (MW, p = 0.035) (Fig. 1C). This indicates that in Drosophila methylation patterns can be rearranged and redistributed between different tissues. There is no significant difference between the heads of male and female adult D. melanogaster (Fig. S1). The presence of higher level of 5mC in the head also eliminates the possibility of methylation being detected due to the possible contamination from gut microflora or endosymbionts as a false positive in Drosophila genomic DNA.

D. melanogaster is a member of the melanogaster group of the subgenus Sophophora and is one of 12 fruit fly species with completely sequenced genome for comparative genomics. There is no date available on the presence of DNA methylation in the other 11 species. In order to assess the distribution of 5mC across genus Drosophila; DNA from the adult stage of twelve prominent member species from subgenera Drosophila and Sophophora was analysed. The bootstrap consensus tree for all the species is shown to provide information on the most frequently appearing branch groupings using the 18S rRNA sequences (original NJ tree and divergence time in Figs. S2 and S3) (Fig. 2A). There is a significant difference between the values of the 5mC amongst the twelve-species analysed (p = 0.0217, KW). The members of subgenus Drosophila carry more 5mC in their genome when compared to the Sophophora (Stage & Eickbush, 2007). Drosophila melanogaster has the lowest while Drosophila persimilis has the highest levels of 5mC amongst the analysed genomes. Our results show that even closely related species show a difference in the levels of DNA methylation; D. simulans and D. sechellia are closely related species from the melanogaster group but have a substantial difference in levels of 5mC in their genome. The levels of 5mC observed across these species do not seem to show any correlation with their phylogenetic relatedness. The members of the melanogaster group posses a diverse profile of global DNA methylation. The lowest level DNA methylation value of 0.001% 5dmC/dC is observed in the genome of D. melanogaster and Drosophila erecta genome has the 0.0765% 5dmC/dC between the members of the melanogaster group. However, the subgenus Drosophila possesses a comparable distribution of 5mC among its members.

From the available genome releases and our data, we have compared the GC content, the values of 5mC and C present and %5mdC/dC for the twelve species (Fig. 2B, Table 2, Figs. S1 and S2). Drosophila grimshawi and Drosophila willistoni possess the lowest number of cytosines in their genomes while Drosophila pseudoobscura has the highest level of cytosines. Despite the lowest GC content, D. grimshawi and D. willistoni have 0.068 and 0.055% 5dmC/dC which is comparable to 0.0495% 5dmC/dC in D. pseudoobscura. Likewise, with a vast difference in the number of 5mC per genome copy, D. melanogaster and D. persimilis have similar genomic GC content (Supplementary File, sheet 3).

D. melanogaster has been identified as one of the DNMT2 only organism, as there is an absence of any other de novo or maintenance methyltransferases (Lyko & Maleszka, 2011). DNMT2 protein from D. melanogaster as the query protein for the BLAST algorithm, similar protein was identified from the other analysed Drosophila species. The sequences with a high identity score between 70–100% and strong E value and at least 95% query coverage were filtered from the obtained results. The multiple sequence alignment of the extracted sequences similar to the DNMT2 of D. melanogaster show strongly conserved regions; they also bear identical secondary structures from the consensus residues aligned using PROMALS3D server (Fig. 3) (Pei, Kim & Grishin, 2008). The possibility of the existence of an unknown methyltransferase or a protein complex can be considered as studies in D. melanogaster embryos with DNMT2 knockout has been shown to have persistence of DNA methylation (Takayama et al., 2014).

Discussion

HPLC-based analysis has shown the presence of 0.034% methylation in a mixed population of w¹¹¹⁸ adult flies and 0.002% 5-methylcytosine/cytosine in adult females of ore-R lab strain in the genome of D. melanogaster. Also, there is a gene-specific distribution of 5mC methylation during D. melanogaster development (Panikar et al., 2017). Our current analysis reports a change in the levels of global DNA methylation using UHPLC/QQQ which allows detection of 5mC with greater accuracy as compared to previously used antibody-based techniques. The method used overcomes limitations of bisulfite-sequencing due to the low concentration of 5mC in Drosophila but does not provide sequence context information on DNA methylation. Hence, we are unable to extrapolate the location of the methylation with respect to annotated genomic features like the transposable elements, promoters, repeats etc.

DNA methylation is present in many insects like hymenopterans, lepidopteran, etc., but is much lower than in mammals and plants (Glastad, Hunt & Goodisman, 2014; Simola et al., 2013; Xiang et al., 2010). The functional importance of DNA methylation in insects is better understood in the eusocial systems like honey bees and wasps (Hunt et al., 2013). The existing evidence suggests that DNA methylation in the eusocial systems delegates the social order by means of alternative splicing or ploidy variation (Glastad et al., 2014; Lyko et al., 2010).

Most Dipterans are known to lack DNMT1, 3A and 3B and appear to possess DNMT2 as the only known DNA methyltransferase (Glastad, Hunt & Goodisman, 2014). Despite reports on the presence of DNA methylation in solitary or non-social insects like stick insects and moths; not much is known about its role and importance. The exact involvement of genomic methylation in molecular processes of Drosophila, if any, remains unexplored.

Conclusion

Our analysis of the complete life cycle of D. melanogaster and eleven other species conclusively establishes the presence of DNA methylation in the members of genus Drosophila. This modification undergoes change during holometabolous development. Also, it suggests that there is no effect from factors like sex, phylogenetic relatedness and genome GC content on the levels of 5mC in Drosophila. Despite the absence of typical (DNMT1 and DNMT 3A/3B) DNA methyltransferases, there is DNA methylation in all twelve species of genus Drosophila. These findings pose an interesting problem that demand further investigation which can lead to the identification of a methyltransferase enzyme with novel functions.

Supplemental Information