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Simultaneous single-molecule epigenetic imaging of DNA methylation and hydroxymethylation.


ABSTRACT: The modifications 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are the two major DNA epigenetic modifications in mammalian genomes and play crucial roles in development and pathogenesis. Little is known about the colocalization or potential correlation of these two modifications. Here we present an ultrasensitive single-molecule imaging technology capable of detecting and quantifying 5hmC and 5mC from trace amounts of DNA. We used this approach to perform single-molecule fluorescence resonance energy transfer (smFRET) experiments which measure the proximity between 5mC and 5hmC in the same DNA molecule. Our results reveal high levels of adjacent and opposing methylated and hydroxymethylated CpG sites (5hmC/5mCpGs) in mouse genomic DNA across multiple tissues. This identifies the previously undetectable and unappreciated 5hmC/5mCpGs as one of the major states for 5hmC in the mammalian genome and suggest that they could function in promoting gene expression.

SUBMITTER: Song CX 

PROVIDER: S-EPMC4843451 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature

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Simultaneous single-molecule epigenetic imaging of DNA methylation and hydroxymethylation.

Song Chun-Xiao CX   Diao Jiajie J   Brunger Axel T AT   Quake Stephen R SR  

Proceedings of the National Academy of Sciences of the United States of America 20160328 16


The modifications 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are the two major DNA epigenetic modifications in mammalian genomes and play crucial roles in development and pathogenesis. Little is known about the colocalization or potential correlation of these two modifications. Here we present an ultrasensitive single-molecule imaging technology capable of detecting and quantifying 5hmC and 5mC from trace amounts of DNA. We used this approach to perform single-molecule fluorescenc  ...[more]

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