Genome-Wide Characterization Of Isoform Switching In Arabidopsis thaliana

Vaneechoutte, D.; Estrada, A. R.; Lin, Y.-C.; Loraine, A.; Vandepoele, K.

doi:10.1101/136770

Home/Archive/bioRxiv

bioRxiv · 10.1101/136770

Genome-Wide Characterization Of Isoform Switching In Arabidopsis thaliana

Vaneechoutte, D.·Estrada, A. R.·Lin, Y.-C.·Loraine, A.·Vandepoele, K.

View original source ↗Export metadata ↓

Abstract

SUMMARYAlternative splicing and the usage of alternate transcription start- or stop sites allows a single gene to produce multiple transcript isoforms. Most plant genes express one isoform at a significantly higher level than others, but under specific conditions this expression dominance can switch to different isoforms. These isoform switches have been observed for thousands of Zea mays and Vitis vinifera genes and have been linked to development and stress response. In Arabidopsis thaliana however, isoform switches have only been reported for 812 genes and the characteristics of these genes, nor the implications of the isoform switches on their protein functions, are currently well understood. Here we present a dataset of isoform dominance and switching for all genes in the AtRTD2 annotation based on a protocol that was benchmarked on simulated data and validated through comparison with a published RT-PCR panel. We report 138,722 isoform switches for 8,162 genes across 206 public RNA-Seq samples and find that these switches change the protein sequences in 23% of the cases. The observed isoform switches show high consistency across replicates and reveal reproducible patterns in response to treatment and development. We also demonstrate that genes with different ages, expression breadths, and functions show large differences in the frequency at which they switch isoforms and in the effect that these isoform switches have on their protein sequences. Finally, we showcase how the detected isoform switches can be applied to gain further insight in the regulation of a genes expression and function.\n\nSIGNIFICANCE STATEMENTIsoform switching through alternative splicing has been reported for thousands of genes in plants, yet genome-wide datasets to study the implications for gene functions are thus far not available. Here we present the first reference dataset of isoform dominance and switching for Arabidopsis thaliana based on 206 public RNA-Seq samples and provide novel insights in the regulation and functional consequences of alternative splicing.

Source connections

Published article ↗

Explore related subjects

plant biology Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Vaneechoutte, D., Estrada, A. R., Lin, Y.-C., Loraine, A., Vandepoele, K.. 2017-05-11. Genome-Wide Characterization Of Isoform Switching In Arabidopsis thaliana. https://doi.org/10.1101/136770

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Photosynthesis-derived carbohydrate supply sustains CuCl2-induced phytoalexin production in rice leaves

Phytoalexins are antimicrobial metabolites whose biosynthesis is triggered by signaling activated by both biotic and abiotic elicitors, but the physiological conditions that sustain their production remain poorly understood. Here, we examined how light and carbohydrate availability affect CuCl2-induced production of diterpenoid (phytocassanes and momilactones) and flavonoid (sakuranetin) phytoalexins in rice (Oryza sativa L.) leaf disks. Darkness strongly suppressed both the accumulation of all three phytoalexin groups and the induction of their biosynthetic genes. In darkness, endogenous sucrose, glucose, and fructose declined to 3%-8% of the levels in the light, whereas early accumulation of jasmonic acid and jasmonoyl-L-isoleucine (JA-Ile) was not detectably reduced. Exogenous sucrose restored phytoalexin accumulation in darkness in a dose-dependent manner, together with the expression of the suppressed biosynthetic genes, whereas equimolar mannitol had no effect. Glucose also restored sakuranetin accumulation in darkness but only partially restored diterpenoid accumulation, whereas the glucose analog 2-deoxy-D-glucose did not, and it suppressed CuCl2-induced accumulation in the light in a dose-dependent manner. In the light, 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), an inhibitor of photosynthetic electron transport, depleted soluble sugars and suppressed phytoalexin accumulation, and sucrose reversed this suppression. Sugars alone induced little phytoalexin accumulation, indicating that carbohydrates act permissively rather than as elicitors. Diterpenoid phytoalexins depended more strongly on light than sakuranetin, yet both classes depended on carbohydrate availability. These results indicate that photosynthesis-derived carbohydrate supply sustains elicitor-induced phytoalexin production in rice leaves and largely accounts for its light dependence.

plant biology↗

bioRxiv2026

Transcriptome analysis provides insights into candidate genetic regulators of birch response to salt stress

Abstract Background: Soil salinization is a worldwide matter of concern and can result in a series of agricultural and ecological problems. Previous transcriptome data have shown genetic regulatory mechanisms of salt stress response in a salt-tolerant species of Betula halophila and a salt-sensitive species of B. platyphylla, but comparative analysis of transcriptional changes in the the two species remains limited. Aims: We compared gene expression in leaves of B. halophila and leaves and roots of B. platyphylla. Methods: Differentially expressed genes (DEGs) were identified after 24 h of salt stress, followed by Gene Ontology enrichment and gene regulatory network (GRN) construction. Selected DEGs were examined by quantitative real-time PCR (RT-qPCR). Results: Compared with 0 h, 956 DEGs were found in B. halophila leaves (BHLeaf), 2,955 in B. platyphylla leaves (BPLeaf), and 3,827 in B. platyphylla roots (BPRoot). BHLeaf DEG expression patterns were similar to those of BPRoot. DEGs from BHLeaf and BPRoot were enriched in cell wall organization or biogenesis, whereas hormone biosynthesis and signaling genes were altered mainly in B. platyphylla. RT-qPCR showed that selected DEGs were induced by 200 mM NaCl for 24 h in B. platyphylla. Conclusions: Our work uncovered genetic mechanisms of salt stress response commonly and uniquely occurring in two birch species and provides resources for breeding salt-tolerant birch.

plant biology↗

bioRxiv2026

Minimal requirements and evolution of polar membrane targeting in the land plant SOSEKI protein family

Accurate spatial distribution of polar proteins is essential for cell function, but mechanisms underlying polar protein targeting in plants are poorly understood. Here, we dissect the molecular mechanisms underlying the polar targeting of the SOSEKI1 (SOK1) protein in Arabidopsis thaliana. Using extensive mutagenesis and truncation analyses of the polarity domain, we mapped the minimal polarity fragment necessary and sufficient for stable polar targeting to a 25-amino-acid region. This region likely forms an amphipathic helix, and mutations reveal that both its polar and apolar faces are essential for membrane association and polarity. Using phylogenetic analysis, we reconstruct the evolutionary history of the minimal polar targeting region across land plants. Using cross-species expression and protein localization, we infer the ancestral polar SOK localization pattern and show how it remained remarkably conserved, only to diversify upon gene duplication. This work identifies a polar targeting peptide in plants, reveals a mechanism for polar membrane targeting of a plant protein family, and demonstrates both conservation and diversification within this family.

plant biology↗