Skip to Main Content
 

Global Search Box

 
 
 

ETD Abstract Container

Abstract Header

In Silico Discovery of Pollen-specific Cis-regulatory Elements in the Arabidopsis Hydroxyproline-Rich Glycoprotein Gene Family

Wolfe, Richard A.
http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1408383003

Abstract Details

2014, Master of Science (MS), Ohio University, Computer Science (Engineering and Technology).
Within every cell is a copy of an organism's DNA. This copy of DNA has all of the information needed for the cell to express every gene in the organism's genome. Although each cell is capable, individual cells do not express every gene in their DNA. The genes expressed by a cell are regulated by transcription factors (TFs) that bind to a transcription factor binding site (TFBS) located in the promoter region of the gene. TFs must bind to TFBSs in order for a gene to be expressed. Tissues are groups of cells that perform a specific function; therefore, the cells of a specific tissue express genes that are not expressed in other cell types. Hydroxyproline-rich glycoprotein (HRGPs) are proteins that are found in the plant cell wall, and they can be further classified according to the degree they are glycosylated as arabinogalactan-proteins (AGPs), extensins (EXTs), and proline-rich proteins (PRPs). Currently, the TFBSs for EXTs, AGPs, and PRPs expressed in the pollen cells of Arabidopsis are unknown andtheir discovery will provide a better understanding of the regulatory and evolutionary processes of these genes. Motif discovery and other bioinformatics tools were used to search the promoter regions of EXT, AGP, and PRP genes expressed in the Arabidopsis pollen cells and select motifs that are putative TFBSs. The best set of motifs discovered as putative pollen-specific TFBSs are GCYAMGKA, ACTMGGAA, CATSAAAMGA, and ATTKGKTTCT. Of the 8 pollen-specific promoters, GCYAMGKA occurs in 5 promoters,ACTMGGAA occurs in 2 promoters, CATSAAAMGA occurs in 4 promoters, and ATTKGKTTCT occurs in 3 promoters. Also, all of the 8 HRGP pollen-specific promoters have anoccurrence of at least one of these four motifs and none of the four motifs occur in the 84 HRGP promoters of genes not expressed in pollen cells.
Lonnie Welch (Advisor)
280 p.
Bioinformatics; Computer Science
Bioinformatics; transcription factor; transcription factor binding site; motif discovery; computer

Recommended Citations

Citations

  • Wolfe, R. A. (2014). In Silico Discovery of Pollen-specific Cis-regulatory Elements in the Arabidopsis Hydroxyproline-Rich Glycoprotein Gene Family [Master's thesis, Ohio University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1408383003

    APA Style (7th edition)

  • Wolfe, Richard. In Silico Discovery of Pollen-specific Cis-regulatory Elements in the Arabidopsis Hydroxyproline-Rich Glycoprotein Gene Family. 2014. Ohio University, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1408383003.

    MLA Style (8th edition)

  • Wolfe, Richard. "In Silico Discovery of Pollen-specific Cis-regulatory Elements in the Arabidopsis Hydroxyproline-Rich Glycoprotein Gene Family." Master's thesis, Ohio University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1408383003

    Chicago Manual of Style (17th edition)

ohiou1408383003
515
© 2014, all rights reserved.
This open access ETD is published by Ohio University and OhioLINK.