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Messenger RNA 3 Prime End Formation in Plants
Department of Plant and Soil Sciences
Gene expression in plants is impacted in many ways by RNA processing. Recent work has magnified the contributions that RNA processing makes to important growth characteristics. This project focuses on one aspect of RNA processing, namely mRNA polyadenylation. Using a broad range of biochemical, genetic, physiological, and genomics approaches, the function of two centrally-situated protein interaction hubs will be determined. Moreover, the contributions that signaling though one of these hubs make to plant growth and development will be assessed. The outcomes of these studies will add new insight into the ways by which plants link envronmental cues with changes in gene expression. This new insight will be valuable for crop scientists who desire to improve plant performance and tolerance to stresses.
2011 Project Description
In the past year, genome-wide sequencing of cDNA fragments that query the mRNA-poly(A) junction has been conducted, using RNA from leaves and seeds as a template for the cDNA. In addition, RNA isolated from the leaves of several Arabidopsis mutants affected in polyadenylation has been used as templates for analogous cDNA fragments. The results of this work suggest a wide-spread occurrence of alternative poly(A) site choice in Arabidopsis, and also indicate that, for some genes, different poly(A) sites are chosen in leaves and seeds.
In addition, they suggest that mutations that alter the functionality of polyadenylation factor subunits need not have widespread and dramatic consequences in terms of polyadenylation efficiency. So-called poly(A) tags have also been produced for alfalfa and Medicago trucatula, as well as alfalfa plants that have been silenced for expression of the alfalfa CPSF30 ortholog.
EVENTS: Research accomplishments have led to presentations at four meetings.
PRODUCTS: This work is a collaboration with bioinformaticists at Miami University in Oxford, OH; as part of this collaboration, there is a continuing development of computational tools for the collection, curation, and analysis of high throughput DNA sequencing data.
DISSEMINATION: A "minicourse" that covers Next Generation DNA sequencing has been developed and was delivered to an undergraduate class at the University of Massachusetts Lowell in May 2011. A seminar dealing with Next Generation DNA sequencing as applied to studies of mRNA polyadenylation was presented to the Dept. of Biology at Juniata College in October 2011.
Two important outcomes flow from the accomplishments of the past year. One is the determination that most Arabidopsis genes possess multiple polyadenylation sites, and that there are degrees of difference in the utilization of these sites during development.
The second is that one Arabidopsis polyadenylation factor subunit, CPSF30, controls poly(A) site choice in more than 80% of all Arabidopsis genes. This discovery has important ramifications for the means by which alternative polyadneylation is linked to signaling stimuli.
Wu, X., Liu, M., Downie, A. B., Liang, C., Ji, G., Li, Q. Q., and Hunt, A. G. (2011) Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation. Proc Natl Acad Sci U S A. 108:12533-12538.
Addepalli, B. and Hunt, A. G. (2011) Diverse Roles of CCCH Zinc Finger Proteins in Stress and Plant Development Responses. In Zinc Fingers: Structure, Properties and Applications. R. Ciofani anL. Makrlik, eds. Nova Science Publishers. In Press.
Hunt, A. G. (2011) RNA Regulatory Elements and Polyadenylation in Plants. Frontiers in Plant Genetics and Genomics, in press.
Hunt, A. G., Ma, L., and Downie, A. B. (2011) Polyadenylation of stored mRNA during seed development. Abstract and presentation at the 2011 Kentucky Innovation and Entrepreneurship Conference, Louisville, KY, May 26, 2011.
Liu, M., Wu, X., Hunt, A. G., and Li, Q. Q. (2011) Lateral Root Development Associated with a Polyadenylation Factor in Arabidopsis. Abstract and presentation at the 2011 International Conference on Arabidopsis Research, Madison, WI, June 22-25, 2011.
Hunt, A. G., Liu, M., Thomas, P. E., Wu, X., and Li, Q. Q. (2011) An Arabidopsis polyadenylation factor subunit coordinates cellular signaling with stress and developmental responses. 2011 Cold Spring Harbor Meeting on Eukaryotic mRNA Processing. Cold Spring Harbor Laboratories, Cold Spring Harbor, NY. August 23-27, 2011.
Dampanaboina, L. and Hunt, A. G. (2011) Characterization of FY, an orthologue of yeast 3' end processing factor Pfs2p, in plant polyadenylation using tethering assay and 3' RACE. Abstract and presentation at the 2011 Rust Belt RNA Meeting, Dayton, OH, October 21-22, 2011.
Gaffney, B., Dinkins, R. D., and Hunt, A. G. (2011) CPSF30 in Medicago. Abstract and presentation at the 2011 Rust Belt RNA Meeting, Dayton, OH, October 21-21, 2011.
Liu, M., Wu, X., Hunt, A. G., and Li, Q. Q. (2011) Lateral Root Development Associated with a Polyadenylation Factor in Arabidopsis. Abstract and presentation at the 2011 Rust Belt RNA Meeting, Dayton, OH, October 21-22, 2011.
Ma, L., Downie, A. B., and Hunt, A. G. (2011) The roles of polyadenylation in seed germination. Abstract and presentation at the 2011 Rust Belt RNA Meeting, Dayton, OH, October 21-22, 2011.