Alternative Splicing Plays a Critical Role in Maintaining Mineral Nutrient Homeostasis in Rice (Oryza sativa)

Abstract

Alternative splicing (AS) of pre-mRNAs promotes transcriptome and proteome diversity and plays important roles in a wide range of biological processes. However, the role of AS in maintaining mineral nutrient homeostasis in plants is largely unknown. To clarify this role, we obtained whole transcriptome RNA sequencing data from rice (Oryza sativa) roots grown in the presence or absence of several mineral nutrients (Fe, Zn, Cu, Mn, and P). Our systematic analysis revealed 13,291 alternatively spliced genes, representing ∼53.3% of the multiexon genes in the rice genome. As the overlap between differentially expressed genes and differentially alternatively spliced genes is small, a molecular understanding of the plant's response to mineral deficiency is limited by analyzing differentially expressed genes alone. We found that the targets of AS are highly nutrient-specific. To verify the role of AS in mineral nutrition, we characterized mutants in genes encoding Ser/Arg (SR) proteins that function in AS. We identified several SR proteins as critical regulators of Zn, Mn, and P nutrition and showed that three SR protein-encoding genes regulate P uptake and remobilization between leaves and shoots of rice, demonstrating that AS has a key role in regulating mineral nutrient homeostasis in rice.

Interactions of gene expression, alternative splicing, and DNA methylation in determining nodule identity

“…We identified 2323 genes that underwent alternative splicing events in at least one nodule developmental stage. Alternative splicing in the nodules appears to be a tightly regulated process because many splicing-related genes are themselves alternatively spliced, including several splicing factors and RNA binding proteins, Our findings are in agreement with several recent reports showing that essential components of the spliceosome undergo alternative splicing and may control the splicing of their own transcripts in response to various developmental and stress signals (Filichkin et al, 2010;Chang et al, 2014;Shen et al, 2014;Thatcher et al, 2016;Calixto et al, 2018;Dong et al, 2018). In addition, genes involved in the NMD surveillance system also experienced alternative splicing.…”

Full-Length Transcriptome Assembly of Italian Ryegrass Root Integrated with RNA-Seq to Identify Genes in Response to Plant Cadmium Stress

“…Ser/Arg (SR)-rich proteins interact with pre-mRNA sequences and splicing factors during spliceosome assembly in order to perform essential functions in constitutive and AS. In rice, three SR protein-encoding genes (SR40, SCL57, and SCL25) regulate P uptake and remobilization between leaves and shoots of rice [53]. However, these studies have mainly focused on model plants using NGS techniques.…”

CuAS: a database of annotated transcripts generated by alternative splicing in cucumbers

“…The transcripts were divided into 12 categories according to the output of Cuffcompare. Then, the following strategies were applied to obtain high-quality transcripts [17,18]. First, all of the transcripts with three class codes (=, j, o) (http://cole-trapnell-lab.github.io/ cufflinks/cuffcompare/) were extracted from the output generated by Cuffcompare.…”