Genome-Wide Analysis of Heat-Sensitive Alternative Splicing in Physcomitrella patens      

Abstract

Plant growth and development are constantly influenced by temperature fluctuations. To respond to temperature changes, different levels of gene regulation are modulated in the cell. Alternative splicing (AS) is a widespread mechanism increasing transcriptome complexity and proteome diversity. Although genome-wide studies have revealed complex AS patterns in plants, whether AS impacts the stress defense of plants is not known. We used heat shock (HS) treatments at nondamaging temperature and messenger RNA sequencing to obtain HS transcriptomes in the moss Physcomitrella patens. Data analysis identified a significant number of novel AS events in the moss protonema. Nearly 50% of genes are alternatively spliced. Intron retention (IR) is markedly repressed under elevated temperature but alternative donor/acceptor site and exon skipping are mainly induced, indicating differential regulation of AS in response to heat stress. Transcripts undergoing heat-sensitive IR are mostly involved in specific functions, which suggests that plants regulate AS with transcript specificity under elevated temperature. An exonic GAG-repeat motif in these IR regions may function as a regulatory cis-element in heat-mediated AS regulation. A conserved AS pattern for HS transcription factors in P. patens and Arabidopsis (Arabidopsis thaliana) reveals that heat regulation for AS evolved early during land colonization of green plants. Our results support that AS of specific genes, including key HS regulators, is fine-tuned under elevated temperature to modulate gene regulation and reorganize metabolic processes.Global warming in recent decades has caused annual temperature extremes that are becoming harmful for all living organisms. Although all living cells show rapid responses to changes of ambient temperature, unlike animals, plants are sessile and cannot escape adverse temperature conditions. Challenged by temperature changes, plants have evolved rapid and complex systems to sense the temperature signal and translate it into cellular defenses for acquired tolerance, such as enhancing protein folding/unfolding activities and maintaining membrane fluidity (Sung et al., 2003). Understanding how plants adapt to temperature stresses has been an important topic in improving thermotolerance in crops.The heat shock response (HSR) is conserved in eukaryotes in response to elevated temperature and induces the activity of heat shock transcription factors (HSFs) to promote the expression of HSR-related genes. Different mechanisms for temperature sensing and signal transduction have been proposed. The general model suggests that constitutively expressed chaperones in the cytoplasm form inactive complexes with HSFs. Upon heat shock (HS), cytosolic chaperones are recruited by misfolded proteins, thus allowing the release of HSFs for phosphorylation, oligomerization, and nuclear localization to regulate gene expression (Mosser et al

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“…org/CoGe/OrganismView.pl), and the coding region was identified by aligning it with the LRE coding sequence. For Physcomitrella patens, the coding sequences of LRE-like genes were identified using RNaseq reads (Chang et al, 2014) in Integrated Genome Browser (http://bioviz.org/igb/index.html). In plants where multiple LRE-like genes were found, the one that shared highest identity with Arabidopsis LRE was chosen for further analysis.…”

Genome-Wide Analysis of Alternative Splicing during Development and Drought Stress in Maize

“…Alternative splicing has recently been implicated as playing a major role in these processes during stresses, including disease, heat, drought, and others (Deom et al, 1987;Iida et al, 2004;Jeong et al, 2011;Kakumanu et al, 2012;Chang et al, 2014;Mandadi and Scholthof, 2015). Gene expression changes in splicing factors are a major factor in determining stress-induced alternative splicing changes (Yan et al, 2012;Leviatan et al, 2013;Staiger and Brown, 2013).…”