Cytosine methylation and hydroxymethylation mark DNA for elimination in Oxytricha trifallax

Genome Biology

Laura F Landweber¹  David H Perlman²  John R Bracht¹ 

[1] Ecology & Evolutionary Biology Department, Princeton University, Washington Rd., Princeton, NJ, 08544, USA;Collaborative Proteomics and Mass Spectrometry Center, Molecular Biology Department and the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Washington Rd., Princeton, NJ, 08544, USA

关键词: decitabine;    azacitidine;    5-azacytidine;    5-Aza-2'-deoxycitidine;    methyltransferase;    heterochromatin;    DNA degradation;    epigenetics;   

Others  :  869398
DOI  :  10.1186/gb-2012-13-10-r99

 received in 2012-06-01, accepted in 2012-10-17,  发布年份 2012

【 摘 要 】

Background

Cytosine methylation of DNA is conserved across eukaryotes and plays important functional roles regulating gene expression during differentiation and development in animals, plants and fungi. Hydroxymethylation was recently identified as another epigenetic modification marking genes important for pluripotency in embryonic stem cells.

Results

Here we describe de novo cytosine methylation and hydroxymethylation in the ciliate Oxytricha trifallax. These DNA modifications occur only during nuclear development and programmed genome rearrangement. We detect methylcytosine and hydroxymethylcytosine directly by high-resolution nano-flow UPLC mass spectrometry, and indirectly by immunofluorescence, methyl-DNA immunoprecipitation and bisulfite sequencing. We describe these modifications in three classes of eliminated DNA: germline-limited transposons and satellite repeats, aberrant DNA rearrangements, and DNA from the parental genome undergoing degradation. Methylation and hydroxymethylation generally occur on the same sequence elements, modifying cytosines in all sequence contexts. We show that the DNA methyltransferase-inhibiting drugs azacitidine and decitabine induce demethylation of both somatic and germline sequence elements during genome rearrangements, with consequent elevated levels of germline-limited repetitive elements in exconjugant cells.

Conclusions

These data strongly support a functional link between cytosine DNA methylation/hydroxymethylation and DNA elimination. We identify a motif strongly enriched in methylated/hydroxymethylated regions, and we propose that this motif recruits DNA modification machinery to specific chromosomes in the parental macronucleus. No recognizable methyltransferase enzyme has yet been described in O. trifallax, raising the possibility that it might employ a novel cytosine methylation machinery to mark DNA sequences for elimination during genome rearrangements.

【 授权许可】

   
2012 Bracht et al.; licensee BioMed Central Ltd.

【 图 表 】

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