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Annotation of retrogenes in Drosophi...

Bai, Yongsheng.

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Annotation of retrogenes in Drosophila and analysis of their expression and newly recruited regulatory regions using computational and comparative genomic approaches.

Record Type:	Language materials, printed : Monograph/item
Title/Author:	Annotation of retrogenes in Drosophila and analysis of their expression and newly recruited regulatory regions using computational and comparative genomic approaches./
Author:	Bai, Yongsheng.
Description:	252 p.
Notes:	Adviser: Esther Betran.
Contained By:	Dissertation Abstracts International68-08B.
Subject:	Biology, Bioinformatics. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3275733
ISBN:	9780549184942

Annotation of retrogenes in Drosophila and analysis of their expression and newly recruited regulatory regions using computational and comparative genomic approaches.
Bai, Yongsheng.

Annotation of retrogenes in Drosophila and analysis of their expression and newly recruited regulatory regions using computational and comparative genomic approaches. - 252 p.

Adviser: Esther Betran.

Thesis (Ph.D.)--The University of Texas at Arlington, 2007.

In this dissertation, retrogenes in Drosophila melanogaster have been annotated in a much more complete way. The origination pattern for retroposition with a bias from the X chromosome to the autosomes in D. melanogaster was confirmed. The analyses allowed the rate at which the retrogenes in the Drosophila genome were recruited during the past &sim;63 million years to be evaluated: 0.5 retrogenes per Myr per lineage. In addition, several recurrent recruitment retroposition events in Drosophila are reported. Analyses of tissue expression indicate that parental genes are expressed more than the retrogenes in all tissues examined with the exception of the Adult Testes (AT). Expression data when considered in the context of retrogene age do not support the "Out of the Testes" hypothesis in Drosophila.

ISBN: 9780549184942Subjects--Topical Terms:

1018415
Biology, Bioinformatics.

Annotation of retrogenes in Drosophila and analysis of their expression and newly recruited regulatory regions using computational and comparative genomic approaches.
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020 $a 9780549184942
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100 1 $a Bai, Yongsheng. $3 1271147
245 1 0 $a Annotation of retrogenes in Drosophila and analysis of their expression and newly recruited regulatory regions using computational and comparative genomic approaches.
300 $a 252 p.
500 $a Adviser: Esther Betran.
500 $a Source: Dissertation Abstracts International, Volume: 68-08, Section: B, page: 4921.
502 $a Thesis (Ph.D.)--The University of Texas at Arlington, 2007.
520 $a In this dissertation, retrogenes in Drosophila melanogaster have been annotated in a much more complete way. The origination pattern for retroposition with a bias from the X chromosome to the autosomes in D. melanogaster was confirmed. The analyses allowed the rate at which the retrogenes in the Drosophila genome were recruited during the past &sim;63 million years to be evaluated: 0.5 retrogenes per Myr per lineage. In addition, several recurrent recruitment retroposition events in Drosophila are reported. Analyses of tissue expression indicate that parental genes are expressed more than the retrogenes in all tissues examined with the exception of the Adult Testes (AT). Expression data when considered in the context of retrogene age do not support the "Out of the Testes" hypothesis in Drosophila.
520 $a Possible recruitment mechanisms for tissue expression pattern and regulatory regions of retrogenes were investigated. Specifically, the possibility of downstream motif inheritance, upstream regulatory elements carry over through aberrant transcription, transposable element donation, neighboring genes co-expression, insertion into a tissue-specific (mainly adult testes) neighborhood, and random enhancer trapping by retrogenes have been explored. My research results support that there is not a particular way in which the retrogenes recruit regulatory regions and that retrogenes do not have the pattern of expression of a random set of insertions. I conclude that either selection in favor of retrogenes expressed in particular patterns, or a few sequence changes fixed under selection, may be necessary in order to produce the regulatory regions and expression patterns observed for the studied retrogenes in Drosophila.
520 $a A detailed analysis of the motifs in the core promoter region of the retrogenes and parental genes with annotated 5' UTR in D. melanogaster also was conducted. Sixteen common motifs reported previously by other authors were explored. With respect to these analyses, I found that retrogenes often have two motifs (DRE and Inr) in their core promoter regions. Additionally, I identified a new over-represented motif in retrogenes, two novel motifs associated with adult testes expression, and another two novel motifs that are over-represented in the set of adult testes-specific retrogenes.
520 $a Finally, a comparative genomics approach was employed to check the conservation of the reported motifs for D. melanogaster in other Drosophila species. Less than 40% (for retrogenes) and 16% (for parental genes) of the motifs found in D. melanogaster are also found in other Drosophila species. Interestingly, some new motifs (15 for retrogenes and 23 for parental genes) have been identified using the phylogenetic footprinting approach. In a consequent transcription factor validation study, a list of genes that contain the reported motifs that could serve as the binding sites for some known transcription factors was compiled. Experimental verification of the functionality of these new motifs will eventually inform the roles these motifs play in specifically regulating retrogenes and may explain retrogene survival.
590 $a School code: 2502.
650 4 $a Biology, Bioinformatics. $3 1018415
650 4 $a Biology, Molecular. $3 1017719
690 $a 0307
690 $a 0715
710 2 $a The University of Texas at Arlington. $3 1025869
773 0 $t Dissertation Abstracts International $g 68-08B.
790 $a 2502
790 1 0 $a Betran, Esther, $e advisor
791 $a Ph.D.
792 $a 2007
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3275733