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Computational identification and cha...

Xi, Hualin.

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Computational identification and characterization of protein-DNA interactions involved in transcriptional regulation.

Record Type:	Language materials, printed : Monograph/item
Title/Author:	Computational identification and characterization of protein-DNA interactions involved in transcriptional regulation./
Author:	Xi, Hualin.
Description:	151 p.
Notes:	Source: Dissertation Abstracts International, Volume: 72-06, Section: B, page: .
Contained By:	Dissertation Abstracts International72-06B.
Subject:	Biology, Molecular. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3451796
ISBN:	9781124569246

Computational identification and characterization of protein-DNA interactions involved in transcriptional regulation.
Xi, Hualin.

Computational identification and characterization of protein-DNA interactions involved in transcriptional regulation. - 151 p.

Source: Dissertation Abstracts International, Volume: 72-06, Section: B, page: .

Thesis (Ph.D.)--Boston University, 2011.

Gene transcription is one of the most essential cellular processes in eukaryotic organism. DNA elements such as cis-elements, enhancers, and insulators as well as various histone modifications and chromatin structures all play important roles in transcriptional regulation. My thesis consists of several projects that took advantage of the recent advance in high-throughput techniques such as ChIP-chip and next-generation sequencing and studied these regulatory mechanisms on a genome-wide scale.

ISBN: 9781124569246Subjects--Topical Terms:

1017719
Biology, Molecular.

Computational identification and characterization of protein-DNA interactions involved in transcriptional regulation.
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100 1 $a Xi, Hualin. $3 1682274
245 1 0 $a Computational identification and characterization of protein-DNA interactions involved in transcriptional regulation.
300 $a 151 p.
500 $a Source: Dissertation Abstracts International, Volume: 72-06, Section: B, page: .
500 $a Adviser: Zhiping Weng.
502 $a Thesis (Ph.D.)--Boston University, 2011.
520 $a Gene transcription is one of the most essential cellular processes in eukaryotic organism. DNA elements such as cis-elements, enhancers, and insulators as well as various histone modifications and chromatin structures all play important roles in transcriptional regulation. My thesis consists of several projects that took advantage of the recent advance in high-throughput techniques such as ChIP-chip and next-generation sequencing and studied these regulatory mechanisms on a genome-wide scale.
520 $a In my first dissertation project, I compiled a set of 723 high quality human core promoter sequences and analyzed for over-represented motifs. Among the ten core promoter motifs identified, two motifs (YY1 and motif8) mostly reside immediately downstream from TSS. In particular, the YY1 motif occurs primarily in genes with short 5'-UTRs and its locations coincide with the translation start site. I validated the binding of YY1 in vivo using a recent ChIP-chip dataset and suggested a dual regulatory role of YY1 in both transcription and translation initiation.
520 $a My second dissertation project was to identify and characterize DNaseI hypersensitive sites (DHS) from DNase-chip experiments. A total of 3904 DHSs were identified from six cell types across 1% of the human genome. A significant number (22%) of DHSs are ubiquitously present among all cell types studied. Surprisingly, nearly all of these ubiquitous DHSs correspond to either promoters or insulator sites that bind CTCF, a protein with enhancer blocking activity. A large number of DHSs were also found to be cell type-specific; these regions are enriched for enhancer elements and correlate with cell type-specific gene expression as well as cell type-specific histone modifications.
520 $a Lastly I conducted an integrated analysis on next-generation sequencing datasets from the ENCODE consortium to identify allele-specific gene expression, protein DNA interactions and epigenetic changes throughout the genome. Using a custom processing workflow, I demonstrated the feasibility of identifying allele-specific events from a single cell line. Well-coordinated allele-specific transcriptional regulation, epigenetic changes and gene expression were observed. An initial survey of genetic variations at the binding sites for 33 TFs showed variations in TF motifs strongly correlated with allele-specific TF binding.
590 $a School code: 0017.
650 4 $a Biology, Molecular. $3 1017719
650 4 $a Biology, Genetics. $3 1017730
650 4 $a Biology, Bioinformatics. $3 1018415
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710 2 $a Boston University. $3 1017454
773 0 $t Dissertation Abstracts International $g 72-06B.
790 1 0 $a Weng, Zhiping, $e advisor
790 $a 0017
791 $a Ph.D.
792 $a 2011
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3451796