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Understanding regulatory sequences v...

Maher, Christopher Andrew.

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Understanding regulatory sequences via comparative genomics.

Record Type:	Electronic resources : Monograph/item
Title/Author:	Understanding regulatory sequences via comparative genomics./
Author:	Maher, Christopher Andrew.
Description:	208 p.
Notes:	Source: Dissertation Abstracts International, Volume: 68-04, Section: B, page: 2485.
Contained By:	Dissertation Abstracts International68-04B.
Subject:	Biology, Genetics. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3258904

Understanding regulatory sequences via comparative genomics.
Maher, Christopher Andrew.

Understanding regulatory sequences via comparative genomics. - 208 p.

Source: Dissertation Abstracts International, Volume: 68-04, Section: B, page: 2485.

Thesis (Ph.D.)--State University of New York at Stony Brook, 2006.

Throughout its life cycle an organism is continually developing and adapting to its environment through alterations in gene expression. Rather than expressing all genes at once, multiple levels of regulation produce an intricate combination of gene expression. Understanding the mechanism of genetic regulation remains a major biological challenge. This research focuses on two distinct levels of genetic regulation: transcriptional and post-transcriptional.Subjects--Topical Terms:

1017730
Biology, Genetics.

Understanding regulatory sequences via comparative genomics.
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100 1 $a Maher, Christopher Andrew. $3 1924326
245 1 0 $a Understanding regulatory sequences via comparative genomics.
300 $a 208 p.
500 $a Source: Dissertation Abstracts International, Volume: 68-04, Section: B, page: 2485.
500 $a Advisers: Lincoln Stein; Doreen Ware.
502 $a Thesis (Ph.D.)--State University of New York at Stony Brook, 2006.
520 $a Throughout its life cycle an organism is continually developing and adapting to its environment through alterations in gene expression. Rather than expressing all genes at once, multiple levels of regulation produce an intricate combination of gene expression. Understanding the mechanism of genetic regulation remains a major biological challenge. This research focuses on two distinct levels of genetic regulation: transcriptional and post-transcriptional.
520 $a To understand protein-DNA based transcriptional regulation, I developed a fast non-alignment based comparative genomics approach to identify highly conserved motifs within upstream sequences of C. elegans and C. briggsae genes expressed in promoter::GFP constructs. I found a resulting set of highly conserved motifs to be enriched in known transcription factor binding sites. It also identified numerous novel motifs that demonstrated tissue-specific enrichment within coregulated genes sets, as defined by the promoter::GFP constructs. Deletion constructs were generated for several of the novel motifs, and preliminary results confirm that these motifs were in fact responsible for the predicted expression patterns. Overall, this approach enabled the rapid identification of regulatory motifs that are responsible for the intricate expression patterns within nematodes.
520 $a At the post-transcriptional level, I explored miRNA-based regulation by comprehensively identifying miRNAs, both paralogous and novel, as well as their respective targets. Analysis of several rapidly evolving families in Arabidopsis thaliana revealed that miRNA genes families arise from a process of genome-wide duplication, tandem duplication, and segmental duplication followed by dispersal and diversification. I demonstrated that many of the highly conserved miRNA gene families have conserved functional roles in development and stress response across species, as defined by similar expression patterns in tissues under a variety of conditions. In addition, many of these highly conserved miRNA genes share conserved genomic locations throughout the divergence of rice and maize, suggesting conservation of their regulatory roles. Last, I used high-throughput sequencing of the small RNA transcriptome to identify novel miRNA genes and characterize their expression patterns. Elucidating the intricate small RNA regulatory network will enable the development of new germplasms for improving crop yields, increased resistance to disease, and adaptation to environmental extremes.
590 $a School code: 0771.
650 4 $a Biology, Genetics. $3 1017730
650 4 $a Engineering, Biomedical. $3 1017684
650 4 $a Biology, Bioinformatics. $3 1018415
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710 2 0 $a State University of New York at Stony Brook. $3 1019194
773 0 $t Dissertation Abstracts International $g 68-04B.
790 1 0 $a Stein, Lincoln, $e advisor
790 1 0 $a Ware, Doreen, $e advisor
790 $a 0771
791 $a Ph.D.
792 $a 2006
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3258904