Chapter title |
Single Base Resolution Analysis of 5-Methylcytosine and 5-Hydroxymethylcytosine by RRBS and TAB-RRBS
|
---|---|
Chapter number | 14 |
Book title |
Cancer Epigenetics
|
Published in |
Methods in molecular biology, January 2015
|
DOI | 10.1007/978-1-4939-1804-1_14 |
Pubmed ID | |
Book ISBNs |
978-1-4939-1803-4, 978-1-4939-1804-1
|
Authors |
Maria A. Hahn, Arthur X. Li, Xiwei Wu, Gerd P. Pfeifer, Hahn MA, Li AX, Wu X, Pfeifer GP, Hahn, Maria A., Li, Arthur X., Wu, Xiwei, Pfeifer, Gerd P. |
Abstract |
Sodium bisulfite-assisted deamination of cytosine forms the basis for conducting single base resolution analysis of 5-methylcytosine in DNA. The TET family of proteins represents a group of enzymes that can oxidize 5-methylcytosine to 5-hydroxymethylcytosine. A modification of the bisulfite-based DNA methylation mapping technique employs TET1-mediated oxidation of 5-methylcytosine (TET-assisted bisulfite sequencing) for single base analysis of 5-hydroxymethylcytosine. Whole genome analysis of cytosine modifications with bisulfite sequencing techniques still is challenging and expensive. Reduced representation bisulfite sequencing (RRBS) has been used to limit the complexity of the analysis to mostly CpG-rich genomic fragments flanked by restriction enzyme cleavage sites, for example MspI (5'CCGG). In this chapter, we describe detailed methods used in our laboratory for analysis of 5-methylcytosine and 5-hydroxymethylcytosine combined (RRBS) and for specific analysis of 5-hydroxymethylcytosine (TAB-RRBS). |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Unknown | 28 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 6 | 21% |
Researcher | 6 | 21% |
Student > Doctoral Student | 3 | 11% |
Student > Master | 3 | 11% |
Professor | 2 | 7% |
Other | 4 | 14% |
Unknown | 4 | 14% |
Readers by discipline | Count | As % |
---|---|---|
Biochemistry, Genetics and Molecular Biology | 11 | 39% |
Agricultural and Biological Sciences | 7 | 25% |
Medicine and Dentistry | 2 | 7% |
Computer Science | 1 | 4% |
Immunology and Microbiology | 1 | 4% |
Other | 1 | 4% |
Unknown | 5 | 18% |