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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.
2010 Project Description
In the past year, a number of research activities have been pursued. It has been determined that the domain on the polyadenylation factor subunit CstF77 to which CPSF30 binds is itself an RNA-binding protein. 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. 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.
Alfalfa lines in which CPSF30 gene expression has been reduced using RNAi technology have been developed; preliminary characterizations of these lines suggests that CPSF30 is important in root growth and development in alfalfa.
Research accomplishments have led to the publication of two peer-reviewed research papers. This work is a collaboration with bioinformaticists at Miami University in Oxford, OH; this collaboration has led to the development of a number of computational tools for the collection, curation, and analysis of high throughput DNA sequencing data.
Two important outcomes flow from the accomplishments of the past year. One is the realization that the site of interaction between two polyadenylation factor subunits - CstF77 and CPSF30 - is likely to be a multifaceted hub of RNA-protein as well as protein-protein interactions. This realization has important ramifications for understanding how polyadenylation might be controlled and altered to change gene expression.
The second is the discovery of an extensive network of alternatively-utilized polyadenylation sites, including sites that are chosen exclusively in seeds or leaves. This network far exceeds the expectations that have been hypothesized in the field, and raises many new possibilities for the regulation of gene expression in plants.
Bell, S. and Hunt, A. G. (2010) The Arabidopsis ortholog of the 77 kD subunit of the polyadenylation Cleavage Stimulatory Factor is an RNA binding protein. FEBS Letters 584, 1449-1454.
Addepalli, B., Limbach, P. A., and Hunt, A. G. (2010) A disulfide linkage in a CCCH zinc finger motif of an Arabidopsis CPSF30 ortholog. FEBS Letters 584, 4408-4412.
Wu, X., Liang, C., Chen, J., Hunt, A. G., and Li, Q. Q. (2010) Alternative and Antisense Polyadenylation in Arabidopsis Revealed by Deep Sequencing. Abstract and presentation at the 2010 Meeting of the Midwest Section of the American Society of Plant Biologists. March 27-28, 2010, Purdue University.
Wu, X., Liang, C., Chen, J., Hunt, A. G., and Li, Q. Q. (2010) Alternative and Antisense Polyadenylation in Arabidopsis Revealed by Deep Sequencing. Abstract and presentation at the 2010 Annual Meeting of the Ohio Bioinformatics Consortium (OCCBIO). June 14-17, 2010, Ohio State University.
Li, Q. Q., Liu, M., Xu, R., and Hunt, A. G. (2010) Calmodulin signaling and mRNA alternative polyadenylation: the developmental connection. Abstract and presentation at the 21st International Conference on Arabidopsis Research, June 6-10, 2010, Yokahama, Japan.
Liu, M., Xu, R., Hunt, A. G., and Li, Q. Q. (2010) AtCPSF30, a Polyadenylation Factor Involved in Multi-developmental Processes, is Functionally Associated with Calmodulin. Abstract and presentation at RNA 2010, June 22-27, 2010, Seattle, WA.
Gaffney, B., Dinkins, R. D., and Hunt, A. G. (2010) CPSF30 in Medicago. Abstract and presentation at the 2010 Rust Belt RNA Meeting, Cleveland, OH, October 22-23, 2010.
Dampanaboina, L., and Hunt, A. G. (2010) Characterization of the plant polyadenylation factor FY. Abstract and presentation at the 2010 Rust Belt RNA Meeting, Cleveland, OH, October 22-23, 2010.