To investigate the effects of SRAS1. The in vitro ubiquitination assays were performed as described previously [ 66 ]. The H 2 O 2 content was measured using a previously reported method [ 67 ]. Expression analysis was carried out with mRNA-seq datasets using Genevestigator. GFP fluorescence left is shown. UBQ10 was used as a reference gene. Gray boxes represent untranslated regions UTRs , White boxes represent exons; line segments represent introns; black arrows represent insertion sites of the sras mutant alleles.
B GO function significant enriched pathway terms. The abscissa is the negative log value of p-value, the ordinate is the first 30 enriched GO terms and function descriptions. C Gene ontology second-level entry frequency chart.
The abscissa is the GO database function description, the ordinate is the number of genes. Different biological functions are shown in red, blue and green bars, respectively. Interactions between SRAS1. The means were calculated from three independent replicates and compared with the no-treatment condition 0 h. The experiments were repeated at least three times with similar results.
C Quantitative analysis of the signal intensity in Fig 7B. The abundance of CSN5A at the 0 hour was set to 1 as a reference for calculating relative abundance of various time point. Then seedlings were treated with or without mM NaCl for 6 h.
Total proteins were extracted from different seedlings. ACTIN served as a loading control. B Quantitative analysis of the signal intensity in A. The abundance of GFP at the 0 mM NaCl treatment was set to 1 as a reference for calculating relative abundance of various time points. We also thank Dr. This is an uncorrected proof. Abstract Increasing evidence points to the tight relationship between alternative splicing AS and the salt stress response in plants.
Author summary High salinity severely affects plant growth and development, impairing crop production worldwide. Introduction Environmental stress dramatically influences plant growth and development [ 1 , 2 ]. Results Two isoforms of RING-type E3 ligase SRAS1 exhibit opposite responses to salt stress Recent studies have demonstrated that plant stress-related genes are particularly prone to AS events, which often modulate the ratio between active and non-active isoforms in response to abiotic stress [ 32 , 33 ].
Download: PPT. The truncated isoform SRAS1. Fig 2. Fig 4. Fig 6. Fig 7. Fig 8. Emerging roles of truncated splicing isoforms in environmental stress adaptation The ubiquitin-proteasome system UPS , including ubiquitin Ub , E1, E2, E3, 26S proteasome, is a rapid mechanism for selective protein degradation and plays crucial roles in plant development and stress tolerance [ 14 , 15 ].
How salt stress triggered and affected AS The recent studies showed that AS was a significant regulatory mechanism in response to salt stress [ 24 , 26 , 53 , 54 ]. Materials and methods Plant material and growth conditions Arabidopsis Arabidopsis thaliana plants used in this study were in the Columbia-0 background.
Subcellular localization For transient expression in N. In vitro ubiquitination assays The in vitro ubiquitination assays were performed as described previously [ 66 ]. Supporting information. S1 Fig. SRAS1 responses to salt stress. S2 Fig. S3 Fig. S4 Fig. S5 Fig. S6 Fig.
The expression levels of CSN5A under salt stress. S7 Fig. S8 Fig. The protein levels of SRAS1. S1 Table. Differentially expressed genes in RNA-seq analysis. S2 Table. The detailed information of SRAS genes. S3 Table. Primers used in this study. S4 Table. References 1. Zhu JK. Abiotic Stress Signaling and Responses in Plants.
Environmental complexity: A buffer against stress in the domestic chick. PLoS One. Caspase-like enzymatic activity and the ascorbate-glutathione cycle participate in salt stress tolerance of maize conferred by exogenously applied nitric oxide.
Plant Signal Behav. Trends Plant Sci. Salt Tolerance Mechanisms of Plants. Annu Rev Plant Biol. The Innovation. Research advances of MYB transcription factors in plant stress resistance and breeding. Mol Cells. Phosphorylation of SOS3-like calcium-binding proteins by their interacting SOS2-like protein kinases is a common regulatory mechanism in Arabidopsis. Plant Physiol. Plant Cell Rep. Targeting salt stress coping mechanisms for stress tolerance in Brassica: A research perspective.
Plant Physiol Biochem. This was performed as described previously The cells were then lysed with SDS lysis buffer and sonicated for 10 minutes using the Diagenode Bioruptor. Sequential ChIP was carried out as described above, except that prior to the first immunoprecipitation, the first antibody was cross-linked to protein A Sepharose beads using disuccinimidyl suberate Pierce to prevent antibody leaching after the first DNA-protein elution from the beads with SDS.
The eluate was then diluted 20 times before being subjected to a second immunoprecipitation overnight with sepharose beads and the respective second antibody.
Normal rabbit IgG was included as a second antibody in an independent sequential ChIP experiment as a control for the estimation of the extent of antibody leaching prior to second immunoprecipitation with antibody against protein of interest. ChIP-Seq was carried out as previously described ChIP-Seq and expression data analysis. All reads were adapter removed and trimmed to 35 bp using trimmomatic Only uniquely mapped reads with an alignment score greater than 10 were kept.
Peaks were identified by MACS 2. To compare expression and binding data, raw read counts within bp around RefSeq promoters were calculated, normalized to total map mass, and background subtracted using the TransView package in R. Animal studies. All mice were monitored daily for signs of morbidity and lymphoma development.
No backcrossing was done. For survival analyses, the Kaplan-Meier method was applied, and the curves were compared using the log-rank test. Changes were considered statistically significant when the P values were less than 0. The data are presented as the mean and standard deviation.
The full statistical analysis is shown in Supplemental Table 4. Study approval. We thank S. Campaner for critical reading of the manuscript and suggestions, B. Al-Haddawi and E. Sim for help with histopathology work. Tergaonkar and E.
Note regarding evaluation of this manuscript: Manuscripts authored by scientists associated with Duke University, The University of North Carolina at Chapel Hill, Duke-NUS, and the Sanford-Burnham Medical Research Institute are handled not by members of the editorial board but rather by the science editors, who consult with selected external editors and reviewers.
Go to JCI Insight. Email the journal. Authorship note: Cheryl M. Koh and Ekta Khattar contributed equally to this work. Abstract Constitutively active MYC and reactivated telomerase often coexist in cancers. Figure 7 Graphical model. View Supplemental data. Conflict of interest: The authors have declared that no conflict of interest exists.
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Mostafavi, H. Variable prediction accuracy of polygenic scores within an ancestry group. The single-cell eQTLGen consortium. Wang, D. Comprehensive functional genomic resource and integrative model for the human brain. Science , eaat Feingold, E. Myers, R. PLoS Biol. Lachmann, A. Bioinformatics 26 , — Deelen, P. Genotype Harmonizer: automatic strand alignment and format conversion for genotype data integration. BMC Res.
Notes 7 , Rumble, S. SHRiMP: accurate mapping of short color-space reads. Purcell, S. PLINK: a tool set for whole-genome association and population-based linkage analyses.
MixupMapper: correcting sample mix-ups in genome-wide datasets increases power to detect small genetic effects. Bioinformatics 27 , — Robinson, M. A scaling normalization method for differential expression analysis of RNA-seq data.
Zerbino, D. Ensembl Nucleic Acids Res. Zaykin, D. Optimally weighted Z -test is a powerful method for combining probabilities in meta-analysis. MacArthur, J. Dobin, A. Bioinformatics 29 , 15—21 Zhu, Z. Chen, E. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics 14 , Kuleshov, M. Enrichr: a comprehensive gene set enrichment analysis web server update.
Massive mining of publicly available RNA-seq data from human and mouse. Yu, G. OMICS 16 , — Javierre, B. Lineage-specific genome architecture links enhancers and non-coding disease variants to target gene promoters. Schofield, E. CHiCP: a web-based tool for the integrative and interactive visualization of promoter capture Hi-C datasets.
Bioinformatics 32 , — Swertz, M. BMC Bioinformatics 11 , S12 Download references. The cohorts participating in this study list their acknowledgements in the cohort-specific sections of the Supplementary Note.
Pierce , R01ES B. Pierce , R35ES B. Pierce and R01CA H. This work was supported by the Sigrid Juselius Foundation J. Kettunen and funds from the Academy of Finland grant numbers and J. We thank K. McIntyre for editing the manuscript text. Patrick Deelen, Morris A. Biao Zeng, Urko M. Roman Kreuzhuber, Willem H.
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