Genome-wide mapping of epigenetic modifications in DNA /

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Bibliographic Details
Author / Creator:Yu, Miao, author.
Ann Arbor : ProQuest Dissertations & Theses, 2015
Description:1 electronic resource (134 pages)
Format: E-Resource Dissertations
Local Note:School code: 0330
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Other authors / contributors:University of Chicago. degree granting institution.
Notes:Advisors: Chuan He Committee members: Bryan C. Dickinson; Lucy A. Godley.
Dissertation Abstracts International, Volume: 77-02(E), Section: B.
Summary:DNA modifications are among the major components in epigenetic regulation of gene expression in both eukaryote and prokaryote. 5-methylcytosine (5mC) and its oxidative derivatives, 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) are present in mammalian genomes while in bacterial genomes N6-methyladenosine (6mA), 5mC and N4-methylcytosine (4mC) are the common DNA modifications. We have been working on the development of high-throughput sequencing methods to locate these DNA modifications in a genome-wide manner and reveal their biological functions. We have developed 1) Tet-assisted bisulfite sequencing (TAB-Seq), a genome-wide approach to map 5hmC at single-base resolution and quantifying the relative abundance of 5hmC. Application of TAB-seq to embryonic stem cells not only confirms widespread distribution of 5hmC in the mammalian genome but also reveals sequence bias and strand asymmetry at 5hmC sites. 2) 4mC-Tet-Assisted Bisulfite-sequencing (4mC-TAB-seq), a next-generation sequencing-coupled method that rapidly and cost efficiently reveals the genome-wide locations of 4mC for bacterial species with an available assembled reference genome. 3) a selective labeling method to map mismatched 5-hydroxymethyluracil (5hmU), which is a key intermediate in one of the proposed active demethylation pathways in mammalian cells.