Single-base resolution analysis of active DNA demethylation using methylase-assisted bisulfite sequencing
| Autor: | Xiaoji Wu, Li Shen, Hao Wu, Yi Zhang |
|---|---|
| Rok vydání: | 2014 |
| Předmět: |
DNA Repair
DNA repair Biomedical Engineering Bioengineering Biology Applied Microbiology and Biotechnology Article Cytosine Mice 03 medical and health sciences chemistry.chemical_compound 0302 clinical medicine Animals Embryonic Stem Cells 030304 developmental biology Demethylation 0303 health sciences Base Sequence High-Throughput Nucleotide Sequencing Methyltransferases DNA Methylation Chromatin Thymine DNA Glycosylase 5-Methylcytosine DNA demethylation Gene Expression Regulation Biochemistry chemistry DNA methylation Molecular Medicine Thymine-DNA glycosylase 030217 neurology & neurosurgery DNA Biotechnology Nucleotide excision repair |
| Zdroj: | Nature biotechnology |
| ISSN: | 1546-1696 1087-0156 |
| DOI: | 10.1038/nbt.3073 |
| Popis: | Active DNA demethylation in mammals involves TET-mediated iterative oxidation of 5-methylcytosine (5mC)/5-hydroxymethylcytosine (5hmC) and subsequent excision repair of highly oxidized cytosine bases 5-formylcytosine (5fC)/5-carboxylcytosine (5caC) by Thymine DNA glycosylase (TDG). However, quantitative and high-resolution analysis of active DNA demethylation activity remains challenging. Here we describe M.SssI methylase-assisted bisulfite sequencing (MAB-seq), a method that directly maps 5fC/5caC at single-base resolution. Genome-wide MAB-seq allows systematic identification of 5fC/5caC in Tdg-depleted embryonic stem cells, thereby generating a base-resolution map of active DNA demethylome. A comparison of 5fC/5caC and 5hmC distribution maps indicates that catalytic processivity of TET enzymes correlates with local chromatin accessibility. MAB-seq also reveals strong strand asymmetry of active demethylation within palindromic CpGs. Integrating MAB-seq with other base-resolution mapping methods enables quantitative measurement of cytosine modification states at key transitioning steps of active demethylation pathway, and reveals a regulatory role of 5fC/5caC excision repair in active DNA demethylation cascade. |
| Databáze: | OpenAIRE |
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