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We treated potato (Solanum tuberosum L.) plantlets with TM and performed gene expression studies to identify genome-wide changes associated with endoplasmic reticulum (ER) stress and the unfolded protein response (UPR). An extensive network of responses was identified, including chromatin remodeling, transcriptional reprogramming, as well as changes in the structural components of the endomembrane network system. Limited genome-wide changes in alternative RNA splicing patterns of protein-coding transcripts were also discovered. Significant changes in RNA metabolism, components of the translation machinery, as well as factors involved in protein folding and maturation occurred, which included a broader set of genes than expected based on Arabidopsis research. Antioxidant defenses and oxygen metabolic enzymes are differentially regulated, which is expected of cells that may be experiencing oxidative stress or adapting to protect proteins from oxidation. Surges in protein kinase expression indicated early signal transduction events. This study shows early genomic responses including an array of differentially expressed genes that have not been reported in Arabidopsis. These data describe novel ER stress responses in a solanaceous host.
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Identification of differential alternative splicing events with an adjusted beta-distribution model
High-throughput next generation sequencing of cDNA, i.e. RNA-Seq, presents an unprecedented resource for characterizing the alternative splicing (AS) in complex eukaryotic transcriptomes. Accumulating evidences indicate that AS is developmentally regulated, but the precise responses of AS event to development is not well understood. Here, we describe a new method, based on an adjusted beta-distribution model, for detection of differential AS patterns from RNA-Seq data comparisons. Applying our method to two datasets of RNA-Seq for zika infection in human cells and pollen tissue in Arabidopsis thaliana, we identified 1,871 differentially AS events for 1,394 protein-coding genes in human and 496 differentially AS events for 358 protein-coding genes in Arabidopsis, respectively. The results included known AS events reported before as well as novel events, which demonstrate that the biological replicates are important in the effective identification using β-distribution. With a high accurate rate, our new method in differential AS identification will facilitate future investigation on transcriptomic annotation.
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- Award ID(s):
- 1557417
- PAR ID:
- 10064246
- Date Published:
- Journal Name:
- IEEE International Conference on Electro Information Technology (EIT)
- Page Range / eLocation ID:
- 276 to 279
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Conference Paper:
- https://doi.org/10.1109/EIT.2017.8053369
