Skip to Main Content
 

Global Search Box

 
 
 

ETD Abstract Container

Abstract Header

GENOME WIDE ANALYSES OF ALTERNATIVE POLYADENYLATION IN ARABIDOPSIS

Guo, Cheng
http://rave.ohiolink.edu/etdc/view?acc_num=miami1479081485753738

Abstract Details

2016, Doctor of Philosophy, Miami University, Cell, Molecular and Structural Biology (CMSB).
This dissertation was initiated to investigate the potential association between DNA methylation and alternative polyadenylation (APA) in Arabidopsis. Through the course of research, other topics derived from this initial study emerged with different perspectives. These four chapters were separately documented in Chapters 2, 3, 4 and 5. In addition, Chapters 1 and 6 provide the overview of introduction and conclusions to the dissertation, respectively. Chapter 2 is focused on studying the association between APA and DNA methylation in Arabidopsis. By analyzing and comparing the poly(A) tag sequencing (PAT-seq) data from met1-3 mutants with their control plants, we observed a global negative correlation between the abundance of DNA methylation and APA, and identified a number of poly(A) clusters (PACs) and genes, whose expression have been affected, which may caused by the loss of CG DNA methylation in the met1-3 mutant. In Chapter 3, we detected and characterized more than 11000 non-3UTR polyadenylation sites (n3PASs) clusters in Arabidopsis genome. Further analyses suggested that the occurrence of these n3PASs were positively correlated with certain characteristics of their respective host genes and surrounding genetic context. In Chapter 4, we conducted a genome wide comparative analysis by characterizing and comparing miniature inverted repeat transposable elements (MITEs) in 19 Arabidopsis thaliana accessions. After acquiring the positional information, we further looked into their potential impacts on genome, regarding the formation of new polyadenylation site and gene expression regulation. In Chapter 5 (a side project), we looked into the expression profiles of siRNAs and miRNAs before and after viral infection in both wild type and transgenic viral resistant rice plants with small RNA high-throughput sequencing data. We confirmed that the newly generated siRNAs, which is the major contributor of the viral resistance, were derived from the engineered inverted repeat construct, and summarized the interplay between siRNAs and miRNAs.
Liang Chun (Advisor)
119 p.
Bioinformatics
Alternative polyadenylation; Arabidopsis; DNA methylation; non3UTR polyadenylation; MITEs

Recommended Citations

Citations

  • Guo, C. (2016). GENOME WIDE ANALYSES OF ALTERNATIVE POLYADENYLATION IN ARABIDOPSIS [Doctoral dissertation, Miami University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=miami1479081485753738

    APA Style (7th edition)

  • Guo, Cheng. GENOME WIDE ANALYSES OF ALTERNATIVE POLYADENYLATION IN ARABIDOPSIS. 2016. Miami University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=miami1479081485753738.

    MLA Style (8th edition)

  • Guo, Cheng. "GENOME WIDE ANALYSES OF ALTERNATIVE POLYADENYLATION IN ARABIDOPSIS." Doctoral dissertation, Miami University, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=miami1479081485753738

    Chicago Manual of Style (17th edition)

miami1479081485753738
535
© 2016, some rights reserved.Creative Commons License GENOME WIDE ANALYSES OF ALTERNATIVE POLYADENYLATION IN ARABIDOPSIS by Cheng Guo is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. Based on a work at etd.ohiolink.edu.
This open access ETD is published by Miami University and OhioLINK.