| Popis: |
Chapter one is an overview of the entire dissertation. In this chapter, I provide background information about current understanding of polyadenylation [poly(A)], poly(A) signals and alternative polyadenylation (APA) in plants and other organisms.Chapter two presents a survey of rice polyadenylation landscape using 55,742 authenticated poly(A) sites. A substantial similarity was found between rice and Arabidopsis in term of cis-elements, suggesting that the polyadenylation machinery is conserved in higher plants. We also found an extensive APA profile in rice where 50% of the genes analyzed have more than one unique poly(A) site and about 4% of the analyzed genes possess alternative poly(A) sites that could result in different protein products.In Chapter three, we analyzed the nuclear mRNA polyadenylation mechanisms in the model alga Chlamydomonas reinhardtii with 16,952 in silico authenticated poly(A) sites. We found an unique and complex poly(A) signal profile that is different from higher plants and mammals. A high level of APA was also found in the Chlamydomonas genome.In Chapter four, we used over 300 million Arabidopsis and rice sequence signatures by Massively Parallel Signature Sequencing (MPSS) and Illumina’s GAII Sequence by Synthesis methods for the analysis of APA and its relationship with differential gene expression. We discovered a large number of genes undergo APA that have not been found previously by other methods. In both species, APA events upstream of stop codons are evident from about 50% of the signatures, corresponding to about 10% of whole transcriptome abundance.Chapter 5 concludes what was discovered in these studies and also gives some future perspectives for the research directions of mRNA polyadenylation in general, particularly in plants. |
