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Characterization of the Building Blo...

Mejia Guerra, Maria Katherine.

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Characterization of the Building Blocks of the Maize Gene Regulatory Grid.

紀錄類型:	書目-電子資源 : Monograph/item
正題名/作者:	Characterization of the Building Blocks of the Maize Gene Regulatory Grid./
作者:	Mejia Guerra, Maria Katherine.
出版者:	Ann Arbor : ProQuest Dissertations & Theses, : 2015,
面頁冊數:	161 p.
附註:	Source: Dissertation Abstracts International, Volume: 78-02(E), Section: B.
Contained By:	Dissertation Abstracts International78-02B(E).
標題:	Bioinformatics. -
電子資源:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=10145142
ISBN:	9781369006933

Characterization of the Building Blocks of the Maize Gene Regulatory Grid.
Mejia Guerra, Maria Katherine.

Characterization of the Building Blocks of the Maize Gene Regulatory Grid. - Ann Arbor : ProQuest Dissertations & Theses, 2015 - 161 p.

Source: Dissertation Abstracts International, Volume: 78-02(E), Section: B.

Thesis (Ph.D.)--The Ohio State University, 2015.

Currently, the study of transcriptional regulation has shifted from focusing on the control of a single or a few genes by one or more regulators to highthroughput studies aimed to understand gene regulation at a genome-wide scale. The overarching goal is to reconstruct the dynamic interactome among regulatory proteins and DNA molecules needed to coordinate the phenotypic output from a given genotype at a resolution that allows depicting the laws governing the causality of the regulatory events and set the bases for fine manipulation of the gene expression phenomenon.

ISBN: 9781369006933Subjects--Topical Terms:

553671
Bioinformatics.

Characterization of the Building Blocks of the Maize Gene Regulatory Grid.
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520 $a Currently, the study of transcriptional regulation has shifted from focusing on the control of a single or a few genes by one or more regulators to highthroughput studies aimed to understand gene regulation at a genome-wide scale. The overarching goal is to reconstruct the dynamic interactome among regulatory proteins and DNA molecules needed to coordinate the phenotypic output from a given genotype at a resolution that allows depicting the laws governing the causality of the regulatory events and set the bases for fine manipulation of the gene expression phenomenon.
520 $a The first step to model transcriptional regulation as a dynamic network is to determine the set of basic blocks minimum required to further determine the topology of the network static counterpart. Traditionally, the characteristics of the components required for the building of gene regulatory networks have been thought as universals. However, large scale projects such as the ENCODE, modENCODE and FANTOM projects have revealed an unprecedented level of variation in trans and cis regulators behaviors among metazoans model organisms.
520 $a In plants, similar coordinated efforts to characterize trans and cisregulators have lagged behind, and as consequence the novelties in transcriptional regulation among plant clades are often ignored. This thesis presents an integrative study for the genome-wide characterization of trans and cis regulators in maize using novel and published data from chromatin immunoprecipitation coupled to next generation sequencing (ChIP-seq), CAPS analysis of gene expression (CAGE), and transcriptomics methods such as microarray and mRNA-seq.
520 $a This works presents a genome-wide characterization of core promoters derived from the mapping of thousands of transcription start sites (TSSs). As a result the boundaries of the annotated genes were redefined as a key step in determine the promoters characteristics. In strong contrast with Arabidopsis and metazoans model organisms, transcriptional initiation appears often confined to a narrow region. In addition, the alternate usage of TSSs across tissues and lines for at least &sim;1500 genes suggest that differential regions flanking the genes can serve as core promoter in a widespread mechanisms for regulation of gene expression.
520 $a Furthermore, the systematic identification of trans-regulators and their study in terms of gene expression, revealed that TFs and co-regulators are mostly widespread expressed across tissues with implications for an increasing in combinatorial regulation. Moreover, the integrative study of ChIP-seq datasets shown a major role for repeats -- often TEs -- in providing TF binding regions, often in the intergenic regions, which might indicate that repeats have been frequently co-opted as cis-regulatory elements.
520 $a Finally, a graph derived from the most confident Protein-DNA interactions observed from ChIP-seq experiments was compiled, and when compared with a randomized version it shows clearly that the expected properties of real-world networks have started to emerge.
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