Poster abstracts

Poster number 20 submitted by Manohar Chakrabarti

Genome wide alternative polyadenylation landscape in the forage legume Red clover (Trifolium pratense L.)

Manohar Chakrabarti (Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546), Randy D. Dinkins (USDA-ARS, Forage-Animal Production Research Unit, Lexington, KY 40546), Arthur G. Hunt (Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546)

Abstract:
Polyadenylation at the 3΄ end of the mRNA is a key step in the mRNA processing with significant bearing on gene expression, mRNA stability, translation ability and others. In recent years evidences are emerging depicting prevalence and role of alternative polyadenylation (APA) on various developmental processes and diseases in humans (Elkon et al., 2013; Shi, 2012). In plants, recent research points towards possible implication of APA on cellular signaling, developmental processes, defense response and oxidative stress tolerance (Chakrabarti and Hunt, 2015; Hunt, 2014). To this end, genome-wide APA analyses of non-model crop species under diverse developmental and physiological conditions are of significant importance. In this study, we have conducted a genome-wide APA analysis of different tissue types of red clover (Trifolium pratense L.), a cool season forage legume, grown widely throughout the northeastern USA.
To this end, poly (A) tag libraries were prepared from leaf, root and flower tissues of red clover using a recently developed protocol (Pati et al., 2015) and were mapped to the red clover genome. The sequence data were used to assemble a list of poly(A) sites, and to study possible occurrences of alternative poly(A) site choice in the three tissues that were sampled. With respect to the latter, evidence supporting the occurrence of tissue-specific APA has been obtained, supporting the hypothesis that tissue-specific APA is an important contributor to regulated gene expression during the development of the plant. Ongoing analyses are focusing on the genomic locations (introns, coding regions, etc.) of PACs displaying tissue-specific APA, and on Gene Ontology (GO) analysis of the genes depicting tissue-specific APA.
This study reveals a genome-wide landscape of APA in a non-model crop species, red clover. Together with previous studies on genome-wide transcriptome analysis of APA in different plants (Wu et al., 2014; Wu et al., 2011), these results will provide comprehensive understanding of the contributions that APA makes to the regulation of gene expression in plants.

References:
1. Chakrabarti, M., and Hunt, A.G. (2015). Biomolecules 5, 1151-1168.
2. Elkon, R., Ugalde, A.P., and Agami, R. (2013). Nat Rev Genet 14, 496-506.
3. Hunt, A.G. (2014). Curr Opin Plant Biol 21, 128-132.
4. Pati, P.K., Ma, L., and Hunt, A.G. (2015). Methods Mol Biol 1255, 159-174.
5. Shi, Y. (2012). RNA 18, 2105-2117.
6. Wu, X., Gaffney, B., Hunt, A.G., and Li, Q.Q. (2014). BMC Genomics 15, 615.
7. Wu, X., Liu, M., Downie, B., Liang, C., Ji, G., Li, Q.Q., and Hunt, A.G. (2011). Proceedings of the National Academy of Sciences, USA 108, 12533-12538.

Keywords: Alternative polyadenylation, red clover, Trifolium