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CpG underrepresentation and the new bacterial CpG specific DNA methyltransferase M.MpeI

ABSTRACT: CpG underrepresentation and the new bacterial CpG specific DNA methyltransferase M.MpeI

PROVIDER: PRJNA175556 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR574869_1.fastq.gz	Fastqsanger.gz
	SRR574869_2.fastq.gz	Fastqsanger.gz
	SRR574870_1.fastq.gz	Fastqsanger.gz
	SRR574870_2.fastq.gz	Fastqsanger.gz
	SRR574871_1.fastq.gz	Fastqsanger.gz

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CpG underrepresentation and the new bacterial CpG specific DNA methyltransferase M.MpeI

Project description:The CpG depleted Mycoplasma penetrans harbors a CpG specific C5 methyltransferase. The aim of this experiment was to confirm the specificity of the methyltransferase in vivo and in vitro. Genomic DNA from Mycoplasma penetrans and Escherichia coli genomic DNA that either was or was not methylated in vitro by M.MpeI were subjected to Illumina MiSeq bisulfite sequencing.

2012-11-29 | E-GEOD-41022 | biostudies-arrayexpress

CpG underrepresentation and the new bacterial CpG specific DNA methyltransferase M.MpeI

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CpG underrepresentation and the bacterial CpG-specific DNA methyltransferase M.MpeI.

Project description:Cytosine methylation promotes deamination. In eukaryotes, CpG methylation is thought to account for CpG underrepresentation. Whether scarcity of CpGs in prokaryotic genomes is diagnostic for methylation is not clear. Here, we report that Mycoplasms tend to be CpG depleted and to harbor a family of constitutively expressed or phase variable CpG-specific DNA methyltransferases. The very CpG poor Mycoplasma penetrans and its constitutively active CpG-specific methyltransferase M.MpeI were chosen for further characterization. Genome-wide sequencing of bisulfite-converted DNA indicated that M.MpeI methylated CpG target sites both in vivo and in vitro in a locus-nonselective manner. A crystal structure of M.MpeI with DNA at 2.15-Å resolution showed that the substrate base was flipped and that its place in the DNA stack was taken by a glutamine residue. A phenylalanine residue was intercalated into the "weak" CpG step of the nonsubstrate strand, indicating mechanistic similarities in the recognition of the short CpG target sequence by prokaryotic and eukaryotic DNA methyltransferases.

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Project description:DNA methyltransferases are primary enzymes for cytosine methylation at CpG sites of epigenetic gene regulation in mammals. De novo methyltransferases DNMT3A and DNMT3B create DNA methylation patterns during development, but how they differentially implement genomic DNA methylation patterns is poorly understood. Here, we report crystal structures of the catalytic domain of human DNMT3B-3L complex, noncovalently bound with and without DNA of different sequences. Human DNMT3B uses two flexible loops to enclose DNA and employs its catalytic loop to flip out the cytosine base. As opposed to DNMT3A, DNMT3B specifically recognizes DNA with CpGpG sites via residues Asn779 and Lys777 in its more stable and well-ordered target recognition domain loop to facilitate processive methylation of tandemly repeated CpG sites. We also identify a proton wire water channel for the final deprotonation step, revealing the complete working mechanism for cytosine methylation by DNMT3B and providing the structural basis for DNMT3B mutation-induced hypomethylation in immunodeficiency, centromere instability and facial anomalies syndrome.

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