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Distinct roles of DNMT1-dependent and –independent methylation patterns in the genome of mouse ES cells

ABSTRACT: We generated base-resolution DNA methylomes of a series of DNMT knockout (KO) ES cells with improved coverage at highly repetitive elements. We find that DNMT1- and DNMT3a/3b-dependent activities actually work complementarily and simultaneously to establish symmetric CG methylation and CHH (H=A, T or C) methylation, and unexpectedly have “division of labor” to suppress retrotransposon long terminal repeats (LTRs) and long interspersed elements (LINEs), respectively. Our data also reveal CG density number of 30 seems like a 'threshold' to predetermine the level of methylation in wild type cells and the magnitude of methylation reduction in KO cells. Only genes with low CG number are either induced or surprisingly suppressed in hypomethylated genome. Our data unveil the concerted action of DNMT enzymes in the establishment/maintenance of methylation patterns. Genomic DNA from four different cell lines were treated with bisulfite and sequenced with the Illumina HiSeq platform using paired end reads.

ORGANISM(S): Mus musculus

SUBMITTER: Zhiguang Li

PROVIDER: E-GEOD-61457 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genomic distribution and inter-sample variation of non-CG methylation across human cell types

Project description:DNA methylation plays an important role in development and disease. The primary sites of DNA methylation in vertebrates are cytosines in the CpG dinucleotide context, which account for roughly three quarters of the total DNA methylation content in human and mouse cells. While the genomic distribution, inter-individual stability and functional role of CpG methylation are reasonably well understood, little is known about DNA methylation targeting CpA, CpC and CpT dinucleotides. Here we report a comprehensive analysis of non-CG methylation in 72 genome-scale DNA methylation maps across human pluripotent and differentiated cell types. We confirm non-CG methylation to be predominant in pluripotent cell types and observe an expected decrease upon differentiation and near complete absence in various differentiated cells. Our data highlight that non-CG methylation is highly variable and shows little conservation between different pluripotent cell lines. While we show a strong correlation of non-CG methylation and DNMT3 expression levels we find a statistical independence of non-CG methylation from pluripotency associated gene expression. Finally, non-CG methylation appears to be spatially correlated with CpG methylation. In summary these results contribute further to our understanding of DNA methylation in human cells and help clarify previous observations using a large representative sample set. Examination of nonCG DNA methylation patterns in pluripotent and differentiated cells

2011-08-31 | E-GEOD-27432 | biostudies-arrayexpress

Distinct roles of DNMT1-dependent and –independent methylation patterns in the genome of mouse ES cells

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2013-12-15 | E-GEOD-51304 | biostudies-arrayexpress

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2016-06-13 | E-GEOD-81436 | biostudies-arrayexpress

Local DNA hypomethylation activates genes in rice endosperm

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2010-11-01 | E-GEOD-22591 | biostudies-arrayexpress

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2016-08-02 | E-GEOD-84103 | biostudies-arrayexpress

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2016-07-03 | E-GEOD-76447 | biostudies-arrayexpress

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