Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes

By Jason T. Huff, Daniel Zilberman. 2014

176 citations recorded by the source corpus.

SUMMARY Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes. Their genomes are typically depleted of CG dinucleotides, because of imperfect repair of deaminated methylcytosines. Here, we extensively surveyed diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless frequently present, catalyzed by a novel DNA methyltransferase family, Dnmt5. Numerous Dnmt5-containing organisms that diverged over a billion years ago exhibit clustered methylation specifically in nucleosome linkers. Clustered methylation occurs at unprecedented densities and directly disfavors nucleosomes, contributing to nucleosome positioning between clusters. Dense methylation is enabled by a novel regime of genomic sequence evolution that enriches CG dinucleotides, driving the highest CG frequencies known. Species with linker methylation have small, transcriptionally active nuclei that approach the physical limits of chromatin compaction. These features constitute a previously unappreciated genome architecture, in which dense methylation influences nucleosome positions, likely facilitating nuclear processes under extreme spatial constraints.

Subfields: Molecular Biology

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In Molecular Biology

1. Dirk Schübeler
2. Jussi Taipale
3. Paul Adrian Ginno
4. P. Beachy
5. Benjamin L. Ebert
6. Siddhartha Jaiswal

Citations in the corpus

• Impact of cytosine methylation on DNA binding specificities of human transcription factors (2017, background): “Nucleosome-associated DNA has a lower rate of methylation than the more accessible linker sequences located between nucleosomes (1, 2).”