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ARS Home » Midwest Area » Lexington, Kentucky » Forage-animal Production Research » Research » Publications at this Location » Publication #350730
Title: Genome-wide atlas of alternative polyadenylation in the forage legume red clover

Author
item CHAKRABARTI, M - University Of Kentucky
item Dinkins, Randy
item HUNT, A - University Of Kentucky

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/5/2018
Publication Date: 7/27/2018
Citation: Chakrabarti, M., Dinkins, R.D., Hunt, A.G. 2018. Genome-wide atlas of alternative polyadenylation in the forage legume red clover. Scientific Reports. 8:11379. 10.1038/s41598-018-29699-7.
DOI: https://doi.org/10.1038/s41598-018-29699-7

Interpretive Summary: Polyadenylation is a post-transcriptional processing step essential for the maturation of the majority of higher animal and plant messenger RNAs (mRNAs). A gene may contain multiple polyadenylation sites and differential usage of these sites gives rise to different distinct mRNAs with the potential to produce different protein products. This phenomenon is termed as ‘alternative polyadenylation’ (APA). There are significant implications of APA in numerous biological processes. Tissue specific occurrences of APA are known to play a regulatory role in humans and plants. Mis-regulation of APA has been attributed as the cause for several human diseases including thalassemia, thrombophilia, muscular dystrophy, and others. Our goal was to characterize tissue specific APA regulation in red clover by comparing expression in leaves, roots and flowers. We identified a number of genes that displayed APA in the different tissues, for example, genes involved in photosynthesis, those implicated in metabolite precursors and energy production were enriched in leaves. A comparison of genes displaying APA in red clover with APA studies done on the model plants Arabidopsis and rice suggest that there is conservation in APA in the genes observed, thus a conserved mechanistic role of the use of APA across plant species. The impact of this work is that it provides for a background that will allow for further characterization of the functional role of regulation of gene expression and production of different proteins in different tissues, and during development, in red clover.

Technical Abstract: A genome-wide analysis of alternative polyadenylation (APA) was carried out in different tissue types in the forage legume red clover. Our analysis revealed increased usage of poly(A) sites that mapped to the introns in leaf and flower tissues as compared to the root. Additionally, poly(A) sites that mapped to protein-coding regions displayed increased usage in leaf and root tissues as compared to the flower. We also identified poly(A) clusters (PACs) and underlying genes displaying APA in different tissues. Genes displaying APA when comparing leaf and flower tissues were enriched for those implicated in responses to water deprivation and genes involved in photosynthesis. Genes depicting APA when comparing leaf and root tissues were enriched for those involved in photosynthesis, genes implicated in generation of precursor metabolites, and energy. Genes manifesting APA when comparing root and flower tissues showed enrichment of genes implicated in protein folding and ribosome biogenesis. Nucleotide composition analysis around poly(A) sites located in different genomic regions in different tissue types showed a high degree of conservation, suggesting that differences in polyadenylation signals are not pivotal factors in determining spatial APA observed in this study. Analysis of spatial expression of genes encoding orthologs of different poly(A) factors in red clover showed significant differential expression of genes encoding orthologs of FIP1(V) and PCFS4, suggesting that these two factors may play a role in regulating spatial APA in red clover. Our analysis also revealed a high degree of conservation of APA events in two the key polyadenylation factors, CPSF30 and FIP1(V) in diverse plant species. Together with our previously reported of spatial gene expression in red clover, this study will provide a comprehensive picture of transcriptome dynamics in this non-model forage legume.