Genome-wide analysis of splicing related genes and alternative splicing in plants

2005 2005

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Abstract (summary)

The phenomenon of pre-mRNA splicing in eukaryotes has been mostly studied in mammalian and yeast systems. The splicing machinery in plants is thought to be largely conserved relative to animal and fungal organisms. This thesis encompasses systematic studies of splicing-related genes and alternative splicing (AS) in plants. A total of 74 snRNA genes and 395 genes encoding splicing related proteins were identified in Arabidopsis, including the previously elusive U4atac snRNA gene. About 50% of the splicing related genes are duplicated in plants. The duplication ratios for splicing regulators are even higher, indicating that the splicing mechanism is generally conserved among plants, but that the regulation of splicing may be more variable and flexible.

Over 30% of the splicing related genes can be alternatively spliced. Overall, both Arabidopsis and rice have about 22% of the expressed genes being alternatively spliced, and both have about 55% AS events to be intron retention (IntronR). The consistent high frequency of IntronR suggests prevalence of splice site recognition by intron definition in plants. 40% of Arabidopsis AS genes are also alternatively spliced in rice, with some examples strongly suggesting a role of the AS event as an evolutionary conserved mechanism of post-transcriptional regulation.

U2AF is an essential splicing factor in animals. The two copies of Arabidopsis U2AF1 (AUSa and AUSb) were experimentally characterized as a case study. AUSa expressed at a higher level than AUSb in most tissues. Altered expression levels of AUSa or AUSb cause pleiotropic phenotypes and splicing pattern changes for some pre-mRNA, indicating the importance of AUSa/b for correct splice site recognition. A novel C-terminal domain (SERE) is highly conserved in all seed plant U2AF1 homologs, suggesting its important function specific to higher plants.

All together, similarities as well as differences were revealed between the splicing mechanisms in plants and mammalians, demonstrating that organisms have evolved special mechanisms to ensure the efficient and accurate splicing in different environments. Two databases (Arabidopsis Splicing Related Genes (ASRG), http://www.plantgdb.org/SRGD/ASRG/, and Alternative Splicing in Plants (ASIP), http://www.plantgdb.org/ASIP/) were constructed for the community to use and will facilitate studies of plant splicing mechanisms.

Indexing (details)

Molecular biology;
0307: Molecular biology
0369: Genetics
Identifier / keyword
Biological sciences; Alternative splicing; Exon skipping; SR protein; Splicing
Genome-wide analysis of splicing related genes and alternative splicing in plants
Wang, Bing-Bing
Number of pages
Publication year
Degree date
School code
DAI-B 66/08, Dissertation Abstracts International
Place of publication
Ann Arbor
Country of publication
United States
9780542261961, 0542261960
Brendel, Volker
Iowa State University
University location
United States -- Iowa
Source type
Dissertations & Theses
Document type
Dissertation/thesis number
ProQuest document ID
Database copyright ProQuest LLC; ProQuest does not claim copyright in the individual underlying works.
Document URL
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