DNA Methylation Changes in a Gene-Specific Manner in Different Developmental Stages of <i>Drosophila melanogaster</i>

Abstract

Although genomic DNA of Drosophila melanogaster has been shown to contain little cytosine methylation, the distribution of this genome-wide methylation patterns in different life stages remains to be elucidated. We have developed an immunochemical method using cDNA microarray to assess methylation. In the present work, this methylation microarray method was employed to identify DNA methylation in and around the genes in different life stages of D. melanogaster. This led to the identification of methylated genes in three stages of D. melanogaster, viz. embryo, pupa and adult. It is noteworthy that there was differential methylation in genes in different life cycle stages. Remarkably, a few functional annotation clusters showed negative correlation between transcription of a particular gene and its methylation status. In this analysis, some of the genes attributed to characteristic biological processes of particular life stage in D. melanogaster were found to be methylated in other life stages. Our analysis while providing a methylation map also suggests that gene-specific DNA methylation is altered during the life cycle stages of D. melanogaster. Keywords:Developmental regulation, DNA methylation, Drosophila development, epigenetics, gene-specific methylation, 5 methyl cytosine.DNA methylation is involved in the regulation of several molecular processes in an eukaryotic system. Methylation plays an important role in gene silencing 1,2 , chromatin remodelling 3 and repression of transposon activity 4 . In vertebrates, X chromosome inactivation and genomic imprinting are influenced by DNA methylation, wherein these phenomena are essential for the normal development of an organism. Invertebrates such as insects show significantly distinct life stages and developmental stagespecific regulation of gene expression which plays a crucial role in the transitions between differentiated lifehistory stages. Many research groups have emphasized the presence of DNA methylation in invertebrates and have advocated that DNA methylation might be the mechanism for developmental gene regulation involved in life cycle transition [5][6][7][8][9][10] . The genome-wide DNA methylation maps of insects like Drosophila melanogaster 9 , Bombyx mori 11 , Solenopsis invicta 12 and Apis mellifera 13,14 have been generated using whole genome bisulphite sequencing. Therefore it is important to study whether these methylation signatures play an important role in life cycle processes in invertebrates.Though Drosophila lacks the canonical DNMT1, DNMT3A and DNMT3B, the presence of very low levels of DNA methylation has been reported in D. melanogaster [15][16][17][18][19][20][21][22] . Presence of methylated DNA has been a controversial issue since few reports suggest that D. melanogaster lacks DNA methylation and DNMT2 is indeed an RNA methyltransferase that uses a DNA methyltransferase type of mechanism [23][24][25] . Capuano et al. 19 employed a sensitive LC-MS/MS method to report the presence of 0.034% cytosine DNA methylation in D. melanogaster...

Single‐base methylome profiling of the giant kelp Saccharina japonica reveals significant differences in DNA methylation to microalgae and plants

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Prospects for incorporation of epigenetic biomarkers in human health and environmental risk assessment of chemicals

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