Dataset Information

Spaceflight-induced alternative splicing during seedling development in Arabidopsis thaliana.

ABSTRACT: Plants grown in spaceflight experience novel environmental signals, including those associated with microgravity and ionizing radiation. Spaceflight triggers a response involving transcriptional re-programming and altered cell morphology, though many aspects of this response remain uncharacterized. We analyzed the spaceflight-induced transcriptome with a focus on genes that undergo alternative splicing to examine differential splicing associated with spaceflight-an unstudied characteristic of the molecular response to spaceflight exposure. RNA sequence data obtained during the APEX03 spaceflight experiment that was collected from two Arabidopsis thaliana ecotypes at two seedling stages grown onboard the International Space Station, or as ground controls at Kennedy Space Center, were re-examined to detect alternative splicing differences induced by spaceflight. Presence/absence variation analysis was used to identify putative expression-level differences in alternatively spliced isoforms between spaceflight and ground controls and was followed by analysis of significant differential alternative splicing. This study provides the first evidence of a role for alternative splicing in the molecular processes of physiological adaptation to the spaceflight environment.

SUBMITTER: Beisel NS

PROVIDER: S-EPMC6447593 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Publications

Spaceflight-induced alternative splicing during seedling development in <i>Arabidopsis thaliana</i>.

Beisel Nicole S NS Noble Jerald J Barbazuk W Brad WB Paul Anna-Lisa AL Ferl Robert J RJ

NPJ microgravity 20190403

Plants grown in spaceflight experience novel environmental signals, including those associated with microgravity and ionizing radiation. Spaceflight triggers a response involving transcriptional re-programming and altered cell morphology, though many aspects of this response remain uncharacterized. We analyzed the spaceflight-induced transcriptome with a focus on genes that undergo alternative splicing to examine differential splicing associated with spaceflight-an unstudied characteristic of th ...[more]

PMID: 30963109

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Project description:Jasmonate is an essential phytohormone regulating plant growth, development, and defense. Alternative splicing (AS) in jasmonate ZIM-domain (JAZ) repressors is well-characterized and plays an important role in jasmonate signaling regulation. However, it is unknown whether other genes in the jasmonate signaling pathway are regulated by AS. We explore the potential for AS regulation in three Arabidopsis genotypes (WT, jaz2, jaz7) in response to methyl jasmonate (MeJA) treatment with respect to: (a) differential AS, (b) differential miRNA targeted AS, and (c) AS isoforms with novel functions. AS events identified from transcriptomic data were validated with proteomic data. Protein interaction networks identified two genes, SKIP and ALY4 whose products have both DNA- and RNA-binding affinities, as potential key regulators mediating jasmonate signaling and AS regulation. We observed cases where AS alone, or AS and transcriptional regulation together, can influence gene expression in response to MeJA. Twenty-one genes contain predicted miRNA target sites subjected to AS, which implies that AS is coupled to miRNA regulation. We identified 30 cases where alternatively spliced isoforms may have novel functions. For example, AS of bHLH160 generates an isoform without a basic domain, which may convert it from an activator to a repressor. Our study identified potential key regulators in AS regulation of jasmonate signaling pathway. These findings highlight the importance of AS regulation in the jasmonate signaling pathway, both alone and in collaboration with other regulators. Significance statement:By exploring alternative splicing, we demonstrate its regulation in the jasmonate signaling pathway alone or in collaboration with other posttranscriptional regulations such as nonsense and microRNA-mediated decay. A signal transduction network model for alternative splicing in jasmonate signaling pathway was generated, contributing to our understanding for this important, prevalent, but relatively unexplored regulatory mechanism in plants.

Dataset Information

Spaceflight-induced alternative splicing during seedling development in Arabidopsis thaliana.

Publications

Spaceflight-induced alternative splicing during seedling development in <i>Arabidopsis thaliana</i>.

Similar Datasets

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