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, repr… Show more
“…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.…”
SUMMARY
Soybean nodulation is a highly controlled process that involves complex gene regulation at both transcriptional and post‐transcriptional levels. In the present study, we profiled gene expression changes, alternative splicing events, and DNA methylation patterns during nodule formation, development, and senescence. The transcriptome data uncovered key transcription patterns of nodule development that included 9669 core genes and 7302 stage‐specific genes. Alternative splicing analysis uncovered a total of 2323 genes that undergo alternative splicing events in at least one nodule developmental stage, with activation of exon skipping and repression of intron retention being the most common splicing events in nodules compared to roots. Approximately 40% of the differentially spliced genes were also differentially expressed at the same nodule developmental stage, implying a substantial association between gene expression and alternative splicing. Genome‐wide‐DNA methylation analysis revealed dynamic changes in nodule methylomes that were specific to each nodule stage, occurred in a sequence‐specific manner, and impacted the expression of 1864 genes. An attractive hypothesis raised by our data is that increased DNA methylation may contribute to the efficiency of alternative splicing. Together, our results provide intriguing insights into the associations between gene expression, alternative splicing, and DNA methylation that may shape transcriptome complexity and proteome specificity in developing soybean nodules.
“…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.…”
SUMMARY
Soybean nodulation is a highly controlled process that involves complex gene regulation at both transcriptional and post‐transcriptional levels. In the present study, we profiled gene expression changes, alternative splicing events, and DNA methylation patterns during nodule formation, development, and senescence. The transcriptome data uncovered key transcription patterns of nodule development that included 9669 core genes and 7302 stage‐specific genes. Alternative splicing analysis uncovered a total of 2323 genes that undergo alternative splicing events in at least one nodule developmental stage, with activation of exon skipping and repression of intron retention being the most common splicing events in nodules compared to roots. Approximately 40% of the differentially spliced genes were also differentially expressed at the same nodule developmental stage, implying a substantial association between gene expression and alternative splicing. Genome‐wide‐DNA methylation analysis revealed dynamic changes in nodule methylomes that were specific to each nodule stage, occurred in a sequence‐specific manner, and impacted the expression of 1864 genes. An attractive hypothesis raised by our data is that increased DNA methylation may contribute to the efficiency of alternative splicing. Together, our results provide intriguing insights into the associations between gene expression, alternative splicing, and DNA methylation that may shape transcriptome complexity and proteome specificity in developing soybean nodules.
“…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.…”
Cadmium (Cd) is a toxic heavy metal element. It is relatively easily absorbed by plants and enters the food chain, resulting in human exposure to Cd. Italian ryegrass (Lolium multiflorum Lam.), an important forage cultivated widely in temperate regions worldwide, has the potential to be used in phytoremediation. However, genes regulating Cd translocation and accumulation in this species are not fully understood. Here, we optimized PacBio ISO-seq and integrated it with RNA-seq to construct a de novo full-length transcriptomic database for an un-sequenced autotetraploid species. With the database, we identified 2367 differentially expressed genes (DEGs) and profiled the molecular regulatory pathways of Italian ryegrass with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis in response to Cd stress. Overexpression of a DEG LmAUX1 in Arabidopsis thaliana significantly enhanced plant Cd concentration. We also unveiled the complexity of alternative splicing (AS) with a genome-free strategy. We reconstructed full-length UniTransModels using the reference transcriptome, and 29.76% of full-length models had more than one isoform. Taken together, the results enhanced our understanding of the genetic diversity and complexity of Italian ryegrass under Cd stress and provided valuable genetic resources for its gene identification and molecular breeding.
“…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.…”
Section: Identification Of Alternative Splicing Events and Isoformsmentioning
Background: Alternative splicing (AS) plays a critical regulatory role in modulating transcriptome and proteome diversity. In particular, it increases the functional diversity of proteins. Recent genome-wide analysis of AS using RNA-Seq has revealed that AS is highly pervasive in plants. Furthermore, it has been suggested that most AS events are subject to tissue-specific regulation.Description: To reveal the functional characteristics induced by AS and tissue-specific splicing events, a database for exploring these characteristics is needed, especially in plants. To address these goals, we constructed a database of annotated transcripts generated by alternative splicing in cucumbers (CuAS: http://cmb.bnu.edu.cn/alt_iso/index.php) that integrates genomic annotations, isoform-level functions, isoform-level features, and tissue-specific AS events among multiple tissues. CuAS supports a retrieval system that identifies unique IDs (gene ID, isoform ID, UniProt ID, and gene name), chromosomal positions, and gene families, and a browser for visualization of each gene.
Conclusion:We believe that CuAS could be helpful for revealing the novel functional characteristics induced by AS and tissue-specific AS events in cucumbers. CuAS is freely available at
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