title: Advances in the profiling of DNA modifications: cytosine methylation and beyond.
abstract: Chemical modifications of DNA have been recognized as key epigenetic mechanisms for maintenance of the cellular state and memory. Such DNA modifications include canonical 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxycytosine (5caC). Recent advances in detection and quantification of DNA modifications have enabled epigenetic variation to be connected to phenotypic consequences on an unprecedented scale. These methods may use chemical or enzymatic DNA treatment, may be targeted or non-targeted and may utilize array-based hybridization or sequencing. Key considerations in the choice of assay are cost, minimum sample input requirements, accuracy and throughput. This Review discusses the principles behind recently developed techniques, compares their respective strengths and limitations and provides general guidelines for selecting appropriate methods for specific experimental contexts.
authors.affiliation: 1] Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92037, USA. [2].
authors.forename: Nongluk
authors.initials: N
authors.lastname: Plongthongkum
authors.affiliation: 1] Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92037, USA. [2].
authors.forename: Dinh H
authors.initials: DH
authors.lastname: Diep
authors.affiliation: Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92037, USA.
authors.forename: Kun
authors.initials: K
authors.lastname: Zhang
mesh_terms: D000465:Algorithms; D000818:Animals; D002874:Chromosome Mapping / Q000379:methods / Q000639:trends; D003596:Cytosine / Q000378:metabolism*; D019175:DNA Methylation; D044127:Epigenesis, Genetic / Q000502:physiology; D020869:Gene Expression Profiling / Q000379:methods / Q000639:trends*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans
chemical_list: D003596:Cytosine