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Genome-wide mapping of epigenetic mo...

Yu, Miao.

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Genome-wide mapping of epigenetic modifications in DNA.

Record Type:	Electronic resources : Monograph/item
Title/Author:	Genome-wide mapping of epigenetic modifications in DNA./
Author:	Yu, Miao.
Description:	134 p.
Notes:	Source: Dissertation Abstracts International, Volume: 77-02(E), Section: B.
Contained By:	Dissertation Abstracts International77-02B(E).
Subject:	Biochemistry. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3724576
ISBN:	9781339080987

Genome-wide mapping of epigenetic modifications in DNA.
Yu, Miao.

Genome-wide mapping of epigenetic modifications in DNA. - 134 p.

Source: Dissertation Abstracts International, Volume: 77-02(E), Section: B.

Thesis (Ph.D.)--The University of Chicago, 2015.

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.

ISBN: 9781339080987Subjects--Topical Terms:

518028
Biochemistry.

Genome-wide mapping of epigenetic modifications in DNA.
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500 $a Source: Dissertation Abstracts International, Volume: 77-02(E), Section: B.
500 $a Adviser: Chuan He.
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520 $a 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.
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