Wide‐ranging transcriptome remodelling mediated by alternative polyadenylation in response to abiotic stresses in Sorghum

• Published in: The Plant journal : for cell and molecular biology 2020-06, Vol.102 (5), p.916-930
• Main Authors: Chakrabarti, Manohar, Lorenzo, Laura, Abdel‐Ghany, Salah E., Reddy, Anireddy S. N., Hunt, Arthur G.
• Format: Article
• Language: English
• Subjects: Abiotic stress; alternative polyadenylation; APA; Cereal crops; Drought; Droughts; Gene expression; Gene Expression Regulation, Plant - genetics; Gene Expression Regulation, Plant - physiology; Gene regulation; Genes; Genomes; heat; mRNA stability; Physiological effects; Plant Proteins - genetics; Plant Proteins - metabolism; Plant Sciences; Polyadenine; Polyadenylation; Polyadenylation - genetics; Polyadenylation - physiology; RNA transport; salinity; Sorghum; Sorghum - genetics; Sorghum - metabolism; Stress; Stress, Physiological - genetics; Stress, Physiological - physiology; Stresses; Transcription; Transcriptome - genetics
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/tpj.14671

Summary Alternative polyadenylation (APA) regulates diverse developmental and physiological processes through its effects on gene expression, mRNA stability, translatability, and transport. Sorghum is a major cereal crop in the world and, despite its importance, not much is known about the role of post‐transcriptional regulation in mediating responses to abiotic stresses in Sorghum. A genome‐wide APA analysis unveiled widespread occurrence of APA in Sorghum in response to drought, heat, and salt stress. Abiotic stress treatments incited changes in poly(A) site choice in a large number of genes. Interestingly, abiotic stresses led to the re‐directing of transcriptional output into non‐productive pathways defined by the class of poly(A) site utilized. This result revealed APA to be part of a larger global response of Sorghum to abiotic stresses that involves the re‐direction of transcriptional output into non‐productive transcriptional and translational pathways. Large numbers of stress‐inducible poly(A) sites could not be linked with known, annotated genes, suggestive of the existence of numerous unidentified genes whose expression is strongly regulated by abiotic stresses. Furthermore, we uncovered a novel stress‐specific cis‐element in intronic poly(A) sites used in drought‐ and heat‐stressed plants that might play an important role in non‐canonical poly(A) site choice in response to abiotic stresses. Significance Statement Our study revealed extensive prevalence of alternative polyadenylation (APA) and elucidated its role in fine‐tuning the regulation of abiotic stress responses and identified a novel stress‐induced G‐rich sequence motif associated with the stress‐induced intronic APA in Sorghum. We also identified a large number of hitherto‐unknown abiotic stress‐responsive transcripts in Sorghum.