Cytosine DNA Methylation Is Found in Drosophila melanogaster but Absent in Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Other Yeast Species

Abstract

The methylation of cytosine to 5-methylcytosine (5-meC) is an important epigenetic DNA modification in many bacteria, plants, and mammals, but its relevance for important model organisms, including Caenorhabditis elegans and Drosophila melanogaster, is still equivocal. By reporting the presence of 5-meC in a broad variety of wild, laboratory, and industrial yeasts, a recent study also challenged the dogma about the absence of DNA methylation in yeast species. We would like to bring to attention that the protocol used for gas chromatography/mass spectrometry involved hydrolysis of the DNA preparations. As this process separates cytosine and 5-meC from the sugar phosphate backbone, this method is unable to distinguish DNA- from RNA-derived 5-meC. We employed an alternative LC–MS/MS protocol where by targeting 5-methyldeoxycytidine moieties after enzymatic digestion, only 5-meC specifically derived from DNA is quantified. This technique unambiguously identified cytosine DNA methylation in Arabidopsis thaliana (14.0% of cytosines methylated), Mus musculus (7.6%), and Escherichia coli (2.3%). Despite achieving a detection limit at 250 attomoles (corresponding to <0.00002 methylated cytosines per nonmethylated cytosine), we could not confirm any cytosine DNA methylation in laboratory and industrial strains of Saccharomyces cerevisiae, Schizosaccharomyces pombe, Saccharomyces boulardii, Saccharomyces paradoxus, or Pichia pastoris. The protocol however unequivocally confirmed DNA methylation in adult Drosophila melanogaster at a value (0.034%) that is up to 2 orders of magnitude below the detection limit of bisulphite sequencing. Thus, 5-meC is a rare DNA modification in drosophila but absent in yeast.

Post-transcriptional gene silencing, transcriptional gene silencing and human immunodeficiency virus

“…In humans, DNMT3 establishes de novo methylation and is responsible for tissue-specific DNA methylation patterns [153,154] . In the case of TGS, recent studies have shown that DNA methylation of CGIs is not required for siRNAguided heterochromatin formation in fission yeast, as was initially described [155] . Similarly, the signatures of TGS in mammals appear to be somewhat diverse and may require DNA methylation in some cases.…”

The Spontaneous Mutation Rate in the Fission Yeast Schizosaccharomyces pombe

“…The S. cerevisiae and S. pombe genomes do not encode a characterized DNA methyltransferase (Becker et al 2012), and neither shows evidence of DNA methylation (Capuano et al 2014) [however, see Tang et al (2012)]. It is therefore interesting that C / T transitions are significantly more common at CpG sites than in the non-CpG context in both S. pombe (x 2 = 70.12, P , 2 3 10 216 ) and S. cerevisiae (Zhu et al 2014).…”

A DNS-metiláció szerepe és megváltozása az öregedés és a daganatos betegségek kialakulása során

“…A gerincteleneknél nem teljeskörűen figyelhető meg a gbM, bizonyos gerinctelen csoportok esetén igen ritka, vagy akár teljesen eltűnhet [16]. Ilyen fajok például az iparban, illetve a kutatásban széleskörűen alkalmazott Saccharomyces cerevisiae vagy a Saccharomyces pombe, amelyek DNS-ében egyáltalán nem fordul elő 5-metilcitozin-módosulás [18]. A Drosophila melanogaster DNSállománya is nagyon alacsony százalékban mutat metiláltságot [18].…”

“…Ilyen fajok például az iparban, illetve a kutatásban széleskörűen alkalmazott Saccharomyces cerevisiae vagy a Saccharomyces pombe, amelyek DNS-ében egyáltalán nem fordul elő 5-metilcitozin-módosulás [18]. A Drosophila melanogaster DNSállománya is nagyon alacsony százalékban mutat metiláltságot [18]. Caenorhabditis elegans esetén szintén hiányzik az 5-metilcitozin [19].…”