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Functional conservation of divergent...

University of California, Berkeley.

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Functional conservation of divergent regulatory sequences: Lessons from Drosophila, scavenger flies, and the true fruit flies.

Record Type:	Language materials, printed : Monograph/item
Title/Author:	Functional conservation of divergent regulatory sequences: Lessons from Drosophila, scavenger flies, and the true fruit flies./
Author:	Hare, Emily Elizabeth.
Description:	126 p.
Notes:	Adviser: Michael B. Eisen.
Contained By:	Dissertation Abstracts International69-09B.
Subject:	Biology, Bioinformatics. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3331641
ISBN:	9780549834625

Functional conservation of divergent regulatory sequences: Lessons from Drosophila, scavenger flies, and the true fruit flies.
Hare, Emily Elizabeth.

Functional conservation of divergent regulatory sequences: Lessons from Drosophila, scavenger flies, and the true fruit flies. - 126 p.

Adviser: Michael B. Eisen.

Thesis (Ph.D.)--University of California, Berkeley, 2008.

Gene expression is precisely regulated by networks of transcription factors that modulate rates of transcriptional by binding enhancers, which integrate spatial and temporal patterning information to specify the tissue fate of a group of cells. Although changes in developmental gene expression play an important role in morphological evolution, the molecular basis for such changes is poorly understood. To characterize the evolutionary dynamics of regulatory sequences and constraints on their function, I constructed and screened fosmid libraries from 12 Acalyptrate fly species and sequenced regions containing important developmental genes. My analyses and functional tests of regulatory regions from these loci are beginning to reveal the constraints on enhancers during evolution.

ISBN: 9780549834625Subjects--Topical Terms:

1018415
Biology, Bioinformatics.

Functional conservation of divergent regulatory sequences: Lessons from Drosophila, scavenger flies, and the true fruit flies.
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020 $a 9780549834625
035 $a (UMI)AAI3331641
035 $a AAI3331641
040 $a UMI $c UMI
100 1 $a Hare, Emily Elizabeth. $3 1018723
245 1 0 $a Functional conservation of divergent regulatory sequences: Lessons from Drosophila, scavenger flies, and the true fruit flies.
300 $a 126 p.
500 $a Adviser: Michael B. Eisen.
500 $a Source: Dissertation Abstracts International, Volume: 69-09, Section: B, page: 5208.
502 $a Thesis (Ph.D.)--University of California, Berkeley, 2008.
520 $a Gene expression is precisely regulated by networks of transcription factors that modulate rates of transcriptional by binding enhancers, which integrate spatial and temporal patterning information to specify the tissue fate of a group of cells. Although changes in developmental gene expression play an important role in morphological evolution, the molecular basis for such changes is poorly understood. To characterize the evolutionary dynamics of regulatory sequences and constraints on their function, I constructed and screened fosmid libraries from 12 Acalyptrate fly species and sequenced regions containing important developmental genes. My analyses and functional tests of regulatory regions from these loci are beginning to reveal the constraints on enhancers during evolution.
520 $a I analyzed a set of enhancers from the eve locus in six sepsid species, in which I showed that the trans-regulatory network governing eve expression was conserved. RNA expression patterns driven by the sepsid enhancers I identified largely overlap the endogenous D. melanogaster eve pattern despite the nearly complete absence of primary sequence or transcription factor binding site conservation, demonstrating that the constraints on enhancer organization are fairly loose. Strikingly, each eve enhancer contains a small number of highly-conserved elements that overlap known functional sites in D. melanogaster and are enriched for pairs of overlapping or adjacent binding sites, suggesting that functional constraint acts on a larger unit than a single binding site.
520 $a The identification of regulatory sequences in animal genomes is still a significant challenge for computational and experimental genomics. Comparative genomic methods that have worked well in vertebrates -- using conservation to predict regulatory function -- have been less successful in Drosophila and other invertebrates. I applied these methods to three species of true fruit flies (Tephritidae) with genomes four to five times larger than D. melanogaster. I showed that there are many discrete non-coding sequences conserved between species and that most have regulatory activity. The success of these methods in tephritids is due to the presence of additional rapidly evolving sequence between functional elements in the larger tephritid genomes. Mapping these conserved elements to the D. melanogaster genome clearly and accurately predicts known regulatory elements using only primary sequence data.
590 $a School code: 0028.
650 4 $a Biology, Bioinformatics. $3 1018415
650 4 $a Biology, Genetics. $3 1017730
650 4 $a Biology, Molecular. $3 1017719
690 $a 0307
690 $a 0369
690 $a 0715
710 2 $a University of California, Berkeley. $3 687832
773 0 $t Dissertation Abstracts International $g 69-09B.
790 $a 0028
790 1 0 $a Eisen, Michael B., $e advisor
791 $a Ph.D.
792 $a 2008
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3331641