A sensitive approach to map genome-wide 5-hydroxymethylcytosine and 5-formylcytosine at single-base resolution
| Autor: | Nan Dai, Zhiyi Sun, Dapeng Sun, Zhenyu Zhu, Yu Zheng, Janine G. Borgaro, Aine Quimby, Ivan R. Corrêa, Shengxi Guan |
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| Rok vydání: | 2014 |
| Předmět: |
Restriction Mapping
Context (language use) Computational biology Biology Genome Epigenesis Genetic Histones 03 medical and health sciences chemistry.chemical_compound Cytosine Mice 0302 clinical medicine Animals Enhancer Molecular Biology Embryonic Stem Cells 030304 developmental biology Gene Library 5-Hydroxymethylcytosine Genetics 0303 health sciences Base Sequence Cell Biology DNA Restriction Enzymes DNA binding site Bisulfite Restriction enzyme CpG site chemistry 5-Methylcytosine 030217 neurology & neurosurgery |
| Zdroj: | Molecular cell. 57(4) |
| ISSN: | 1097-4164 |
| Popis: | Mapping genome-wide 5-hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC) at single-base resolution is important to understand their biological functions. We present a cost-efficient mapping method that combines 5hmC-specific restriction enzyme PvuRts1I with a 5hmC chemical labeling enrichment method. The sensitive method enables detection of low-abundance 5hmC sites, providing a more complete 5hmC landscape than available bisulfite-based methods. This method generated a genome-wide 5fC map at single-base resolution. Parallel analyses revealed that 5hmC and 5fC in non-CpG context exhibit lower abundance, more dynamically, than those in CpG context. In the genic region, distribution of 5hmCpG and 5fCpG differed from 5hmCH and 5fCH (H = A, T, C). 5hmC and 5fC were distributed distinctly at regulatory protein-DNA binding sites, depleted in permissive transcription factor binding sites, and enriched at active and poised enhancers. This sensitive bisulfite conversion-free method can be applied to biological samples with limited starting material or low-abundance cytosine modifications. |
| Databáze: | OpenAIRE |
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