High-Resolution Enzymatic Mapping of Genomic 5-Hydroxymethylcytosine in Mouse Embryonic Stem Cells

Autor: Sriharsa Pradhan, Xiaodong Cheng, Yiwei Liu, Ling Yu, Jolyon Terragni, Hua Wang, Zhenyu Zhu, Yu Zheng, Zhiyi Sun, Dapeng Sun, Janine G. Borgaro, Shengxi Guan
Jazyk: angličtina
Rok vydání: 2013
Předmět:
Histone H3 Lysine 4
Cell
High resolution
Hydroxylation
General Biochemistry
Genetics and Molecular Biology
Article
Cell Line
Histones
03 medical and health sciences
chemistry.chemical_compound
Cytosine
Mice
0302 clinical medicine
medicine
Animals
Epigenetics
Enhancer
lcsh:QH301-705.5
Embryonic Stem Cells
030304 developmental biology
chemistry.chemical_classification
5-Hydroxymethylcytosine
0303 health sciences
biology
030302 biochemistry & molecular biology
Chromosome Mapping
Computational Biology
DNA Restriction Enzymes
Genomics
Sequence Analysis
DNA
DNA Methylation
Embryonic stem cell
Molecular biology
Cell biology
medicine.anatomical_structure
Enzyme
Histone
chemistry
CpG site
lcsh:Biology (General)
CTCF
030220 oncology & carcinogenesis
DNA methylation
biology.protein
5-Methylcytosine
CpG Islands
Zdroj: Cell Reports, Vol 3, Iss 3, p 968 (2013)
Cell Reports, Vol 3, Iss 2, Pp 567-576 (2013)
ISSN: 2211-1247
Popis: SummaryWe describe the use of a unique DNA-modification-dependent restriction endonuclease AbaSI coupled with sequencing (Aba-seq) to map high-resolution hydroxymethylome of mouse E14 embryonic stem cells. The specificity of AbaSI enables sensitive detection of 5-hydroxymethylcytosine (5hmC) at low-occupancy regions. Bioinformatic analysis suggests 5hmCs in genic regions closely follow the 5mC distribution. 5hmC is generally depleted in CpG islands and only enriched in a small set of repetitive elements. A regularly spaced and oscillating 5hmC pattern was observed at the binding sites of CTCF. 5hmC is enriched at the poised enhancers with the monomethylated histone H3 lysine 4 (H3K4me1) marks, but not at the active enhancers with the acetylated histone H3 lysine 27 (H3K27Ac) marks. Non-CG hydroxymethylation appears to be prevalent in the mitochondrial genome. We propose that some amounts of transiently stable 5hmCs may indicate a poised epigenetic state or demethylation intermediate, whereas others may suggest a locally accessible chromosomal environment for the TET enzymatic apparatus.
Databáze: OpenAIRE
Externí odkaz: