Genome methylation in D. melanogaster is found at specific short motifs and is independent of DNMT2 activity

Abstract

Cytosine methylation in the genome of Drosophila melanogaster has been elusive and controversial: Its location and function have not been established. We have used a novel and highly sensitive genomewide cytosine methylation assay to detect and map genome methylation in stage 5 Drosophila embryos. The methylation we observe with this method is highly localized and strand asymmetrical, limited to regions covering ∼1% of the genome, dynamic in early embryogenesis, and concentrated in specific 5-base sequence motifs that are CA- and CT-rich but depleted of guanine. Gene body methylation is associated with lower expression, and many genes containing methylated regions have developmental or transcriptional functions. The only known DNA methyltransferase in Drosophila is the DNMT2 homolog MT2, but lines deficient for MT2 retain genomic methylation, implying the presence of a novel methyltransferase. The association of methylation with a lower expression of specific developmental genes at stage 5 raises the possibility that it participates in controlling gene expression during the maternal-zygotic transition.

Transcriptome-wide distribution and function of RNA hydroxymethylcytosine

“…For ease of interpreting results, we analyzed hmrC in Drosophila melanogaster because (i) cytosine methylation in Drosophila DNA is either absent or very low, being restricted to specific cellular contexts (6,7), and (ii) we have found no evidence of DNA hydroxymethylation in this organism ( fig. S1).…”

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

“…Recently LC-MS/MS and the immuno-precipitation prior to bisulphite conversion studies have reported the presence of DNA methylation in D. melanogaster genome 19,20 . Substantial evidence suggests that immunoaffinity based methods could find application in detecting DNA methylation in D. melanogaster 27,31 .…”

“…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. DNA methylation in embryonic stage 5 of D. melanogaster was demonstrated by employing immuno-precipitation and bisulphite sequencing 20 . These observations indicate that immuno-affinity based assays using anti-5-methyl cytosine antibodies have led to detection of DNA methylation in D. melanogaster 15,20,[26][27][28][29][30] .…”

“…DNA methylation in embryonic stage 5 of D. melanogaster was demonstrated by employing immuno-precipitation and bisulphite sequencing 20 . These observations indicate that immuno-affinity based assays using anti-5-methyl cytosine antibodies have led to detection of DNA methylation in D. melanogaster 15,20,[26][27][28][29][30] . Although 5-cytosine methylation has been detected in different life stages of D. melanogaster 15,16,20 , information on methylome map across the different life cycle stages of D. melanogaster is lacking.…”