5-Methylcytosine is not detectable in Saccharomyces cerevisiae DNA.

Proffitt, J H; Davie, James R.; Swinton, David; Hattman, Stanley

doi:10.1128/mcb.4.5.985

Cited by 168 publications

(101 citation statements)

References 17 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In fungi, m5C is concentrated in repeat loci whereas active genes are not methylated 6,9 . Furthermore, several model eukaryotes are devoid of DNA methylation altogether, including the yeast Saccharomyces cerevisiae 12 , the nematode Caenorhabditis elegans 13 , the fruit fly Drosophila melanogaster 14 (except in the early stages of embryogenesis 15 ) and the brown alga Ectocarpus siliculosus 16 . From the methylomes examined thus far, it is therefore unclear which are the ancestral underlying mechanisms at work and those that have been co-opted to distinct biological roles in different eukaryotic groups.…”

mentioning

confidence: 99%

Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum

et al. 2013

View full text Add to dashboard Cite

DNA cytosine methylation is a widely conserved epigenetic mark in eukaryotes that appears to have critical roles in the regulation of genome structure and transcription. Genome-wide methylation maps have so far only been established from the supergroups Archaeplastida and Unikont. Here we report the first whole-genome methylome from a stramenopile, the marine model diatom Phaeodactylum tricornutum. Around 6% of the genome is intermittently methylated in a mosaic pattern. We find extensive methylation in transposable elements. We also detect methylation in over 320 genes. Extensive gene methylation correlates strongly with transcriptional silencing and differential expression under specific conditions. By contrast, we find that genes with partial methylation tend to be constitutively expressed. These patterns contrast with those found previously in other eukaryotes. By going beyond plants, animals and fungi, this stramenopile methylome adds significantly to our understanding of the evolution of DNA methylation in eukaryotes.

show abstract

mentioning

confidence: 99%

Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum

et al. 2013

View full text Add to dashboard Cite

show abstract

“…In addition, two environments (cCg and tCg) show additional elevations in mutation rate. (39)(40)(41). However, a recent study using air chromatography found ∼0.364% methylation at cytosines in S. cerevisiae (42).…”

Section: Discussionmentioning

confidence: 99%

Precise estimates of mutation rate and spectrum in yeast

Zhu

Siegal

Hall

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

397

444

View full text Add to dashboard Cite

Mutation is the ultimate source of genetic variation. The most direct and unbiased method of studying spontaneous mutations is via mutation accumulation (MA) lines. Until recently, MA experiments were limited by the cost of sequencing and thus provided us with small numbers of mutational events and therefore imprecise estimates of rates and patterns of mutation. We used whole-genome sequencing to identify nearly 1,000 spontaneous mutation events accumulated over ∼311,000 generations in 145 diploid MA lines of the budding yeast Saccharomyces cerevisiae. MA experiments are usually assumed to have negligible levels of selection, but even mild selection will remove strongly deleterious events. We take advantage of such patterns of selection and show that mutation classes such as indels and aneuploidies (especially monosomies) are proportionately much more likely to contribute mutations of large effect. We also provide conservative estimates of indel, aneuploidy, environment-dependent dominant lethal, and recessive lethal mutation rates. To our knowledge, for the first time in yeast MA data, we identified a sufficiently large number of single-nucleotide mutations to measure context-dependent mutation rates and were able to (i) confirm strong AT bias of mutation in yeast driven by high rate of mutations from C/G to T/A and (ii) detect a higher rate of mutation at C/G nucleotides in two specific contexts consistent with cytosine methylation in S. cerevisiae.neighbor-dependent mutation rate | strongly deleterious mutation S pontaneous mutations are the source of all genetic variation in nature. The rate of emergence of new mutations and the relative proportions of advantageous, neutral, and deleterious mutations are key determinants in how species evolve and adapt to new selective challenges. Unfortunately, our knowledge of the properties of spontaneous mutations remains incomplete primarily due to the difficulty of observing large enough numbers of mutational events in an unbiased way.Analyzing patterns of divergence in nonfunctional sequences is a statistically powerful method used to study relative rates of different mutation classes. This method is applicable to most organisms and now can generally be carried out on a genomewide scale. However, this approach relies crucially on the assumption that mutations in certain regions, such as pseudogenes or fourfold degenerate codon positions, are not affected by selection and are thus reliable approximations of true mutation rate. It is now becoming apparent that selection or selectionlike processes, such as biased gene conversion, are acting even at these sequences and can substantially bias the observed patterns (1-5).Studies focusing on mutations in reporter genes use a more restrictive method that can be applied only in model organisms. In some cases, such reporter genes can be placed genome-wide and thus provide estimates of genomic variation in mutation rates. However, this approach is limited by the inability to detect mutations without a visible phenotype and thus ...

show abstract

“…Although DNA methylation at CpG dinucleotides is a general phenomenon of eukaryotic genomes, methylated CpG residues have not been found in several well-known genetic model systems, such as the yeast, C. elegans, and Drosophila (23)(24)(25). Evidence for expression of CpG MTase(s) in these organisms also has been lacking.…”

Section: Discussionmentioning

confidence: 99%

“…In contrast to the vertebrates, the genomes of Drosophila, Caenorhabditis elegans, and yeast are deficient in m 5 C residues, at least at the resolution level of HPLC analyses (23)(24)(25). Evidence for the existence of CpG MTase-like proteins in these organisms also is lacking (see Discussion).…”

mentioning

confidence: 99%

Drosophila proteins related to vertebrate DNA (5-cytosine) methyltransferases

Hung

Karthikeyan

Huang

et al. 1999

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

DNA methylation at CpG residues is closely associated with a number of biological processes during vertebrate development. Unlike the vertebrates, however, several invertebrate species, including the Drosophila, do not have apparent DNA methylation in their genomes. Nor have there been reports on a DNA (5-cytosine) methyltransferase (CpG MTase) found in these invertebrates. We now present evidence for two CpG MTase-like proteins expressed in Drosophila cells. One of these, DmMTR1, is a protein containing peptide epitopes immunologically related to the conserved motifs I and IV in the catalytic domain of the mammalian dnmt1. DmMTR1 has an apparent molecular mass of 220 kDa and, similar to mammalian dnmt1, it also interacts in vivo with the proliferating cell nuclear antigen. During interphase of the syncytial Drosophila embryos, the DmMTR1 molecules are located outside the nuclei, as is dnmt1 in the mouse blastocyst. However, DmMTR1 appears to be rapidly transported into, and then out of the nuclei again, as the embryos undergo mitotic waves. Immunofluorescent data indicate that DmMTR1 molecules ''paint'' the whole set of condensed Drosophila chromosomes throughout the mitotic phase, suggesting they may play an essential function in the cell-cycle regulated condensation of the Drosophila chromosomes. Through search in the genomic database, we also have identified a Drosophila polypeptide, DmMT2, that exhibits high sequence homology to the mammalian dnmt2 and the yeast CpG MTase homolog pmt1. The expression of DmMT2 appears to be developmentally regulated. We discuss the evolutionary and functional implications of the discovery of these two Drosophila proteins related to mammalian CpG MTases.epitope detection ͉ early embryo ͉ cell cycle ͉ chromatin structure ͉ database

show abstract

5-Methylcytosine is not detectable in Saccharomyces cerevisiae DNA.

Cited by 168 publications

References 17 publications

Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum

Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum

Precise estimates of mutation rate and spectrum in yeast

Drosophila proteins related to vertebrate DNA (5-cytosine) methyltransferases

Contact Info

Product

Resources

About