Discovery and Expression Analysis of Alternative Splicing Events Conserved among Plant SR Proteins

Rauch, Hypaitia B.; Patrick, Tara L.; Klusman, Katarina M.; Battistuzzi, Fabia U.; Mei, Wenbin; Brendel, Volker; Lal, Sadhna

doi:10.1093/molbev/mst238

Cited by 39 publications

(35 citation statements)

References 40 publications

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“…AS events were detected in SR proteins, confirming previous observations (Kalyna et al 2006;Rauch et al 2014;Chamala et al 2015). Out of 21 SR proteins in maize, 19 demonstrate AS, and 13 of these have 24 conserved AS events with other species, including 13 IntronR, four AltA, four AltD, and three ExonS events (Table S5).…”

Section: Conserved As Is More Common Among Single Copy Genessupporting

confidence: 87%

“…Maize SR protein genes were retrieved from Rauch et al (2014); Sorghum SR protein genes were retrieved from Richardson et al (2011). Maize hnRNP protein encoding genes were retrieved from PlantGDB (Duvick et al 2008).…”

Section: Conserved As In Sr and Hnrnp Proteinsmentioning

confidence: 99%

“…AS has been observed in the hnRNP and SR protein splicing factor gene families (Kalyna et al 2006;Rauch et al 2014;Chamala et al 2015), and has been associated with plant stress (Staiger and Brown 2013). We specifically examined the SR and hnRNP genes for conserved AS events to identify isoforms that may be important for the proper function and regulation of these important splice factors, and to provide a platform to examine differences in AS between species.…”

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confidence: 99%

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Evolutionarily Conserved Alternative Splicing Across Monocots

et al. 2017

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One difficulty when identifying alternative splicing (AS) events in plants is distinguishing functional AS from splicing noise. One way to add confidence to the validity of a splice isoform is to observe that it is conserved across evolutionarily related species. We use a high throughput method to identify junction-based conserved AS events from RNA-Seq data across nine plant species, including five grass monocots (maize, sorghum, rice, Brachpodium, and foxtail millet), plus two nongrass monocots (banana and African oil palm), the eudicot Arabidopsis, and the basal angiosperm Amborella. In total, 9804 AS events were found to be conserved between two or more species studied. In grasses containing large regions of conserved synteny, the frequency of conserved AS events is twice that observed for genes outside of conserved synteny blocks. In plant-specific RS and RS2Z subfamilies of the serine/arginine (SR) splicefactor proteins, we observe both conservation and divergence of AS events after the whole genome duplication in maize. In addition, plant-specific RS and RS2Z splice-factor subfamilies are highly connected with R2R3-MYB in STRING functional protein association networks built using genes exhibiting conserved AS. Furthermore, we discovered that functional protein association networks constructed around genes harboring conserved AS events are enriched for phosphatases, kinases, and ubiquitylation genes, which suggests that AS may participate in regulating signaling pathways. These data lay the foundation for identifying and studying conserved AS events in the monocots, particularly across grass species, and this conserved AS resource identifies an additional layer between genotype to phenotype that may impact future crop improvement efforts.

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Section: Conserved As Is More Common Among Single Copy Genessupporting

confidence: 87%

Section: Conserved As In Sr and Hnrnp Proteinsmentioning

confidence: 99%

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confidence: 99%

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Evolutionarily Conserved Alternative Splicing Across Monocots

et al. 2017

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“…An additional intron is generated in the 3′ UTR region of zm-SC30. Interestingly, that 3′ UTR intron splice isoform introduces a PTC leading to the nonsense mediated decay, and this intron retention event in the 3′ UTR is evolutionary conserved across different plant species (Rauch et al, 2014). We detected the same intron retention event in the 3′ UTR (Supplemental Figure 9) and further demonstrate that expression level of two isoforms (GRMZM2G016296_asmbl_188362 and GRMZM2G016296_asmbl_188364, which spliced that 3′ UTR intron), are decreased during stress (Supplemental Table 4).…”

Section: Discussionmentioning

confidence: 99%

A Comprehensive Analysis of Alternative Splicing in Paleopolyploid Maize

et al. 2017

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Identifying and characterizing alternative splicing (AS) enables our understanding of the biological role of transcript isoform diversity. This study describes the use of publicly available RNA-Seq data to identify and characterize the global diversity of AS isoforms in maize using the inbred lines B73 and Mo17, and a related species, sorghum. Identification and characterization of AS within maize tissues revealed that genes expressed in seed exhibit the largest differential AS relative to other tissues examined. Additionally, differences in AS between the two genotypes B73 and Mo17 are greatest within genes expressed in seed. We demonstrate that changes in the level of alternatively spliced transcripts (intron retention and exon skipping) do not solely reflect differences in total transcript abundance, and we present evidence that intron retention may act to fine-tune gene expression across seed development stages. Furthermore, we have identified temperature sensitive AS in maize and demonstrate that drought-induced changes in AS involve distinct sets of genes in reproductive and vegetative tissues. Examining our identified AS isoforms within B73 × Mo17 recombinant inbred lines (RILs) identified splicing QTL (sQTL). The 43.3% of cis-sQTL regulated junctions are actually identified as alternatively spliced junctions in our analysis, while 10 Mb windows on each side of 48.2% of trans-sQTLs overlap with splicing related genes. Using sorghum as an out-group enabled direct examination of loss or conservation of AS between homeologous genes representing the two subgenomes of maize. We identify several instances where AS isoforms that are conserved between one maize homeolog and its sorghum ortholog are absent from the second maize homeolog, suggesting that these AS isoforms may have been lost after the maize whole genome duplication event. This comprehensive analysis provides new insights into the complexity of AS in maize.

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“…The SR protein homolog TgSR3 was shown to affect the AS of over 10,000 genes in Toxoplasma gondii 15. In addition, the high frequency of AS among the SR family of proteins in plants has been linked to important roles in gene regulation during development and in response to environmental stress16.…”

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Identified of a novel cis-element regulating the alternative splicing of LcDREB2

Liu

Yuan

Liu

et al. 2017

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Alternative splicing (AS) is an important gene regulation mechanism in plants. Despite the widespread use of AS in plant gene expression regulation, the identification of the cis-elements involved in the AS mechanism is rarely reported in plants. To explore the regulation mechanism of the AS of LcDREB2, a DREB2 ortholog from Sheepgrass (Leymus chinensis), the genomic sequences of LcDREB2 and its homologs in Poaceae were aligned, and six mutations were introduced in the conserved sequence of LcDREB2. By analyzing the distinct transcript patterns of the LcDREB2 mutants in transgenic Oryza sativa, a novel cis-element that affected the AS of LcDREB2 was identified as Exonic Splicing Enhancer 1 (ESE1). In addition, five serine-arginine rich (SR) proteins were confirmed to interact with ESE1 by electrophoretic mobility shift assay (EMSA). To further explore the expression regulation mechanism of the DREB subfamily, phylogenetic analysis of DREB2 paralogous genes was performed. The results strongly supported the hypothesis that AS is conserved in Poaceae plants and that it is an evolutionary strategy for the regulation of the functional expression of genes. The findings and methods of our study will promote a substantial step forward in understanding of the plant AS regulation mechanism.

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Discovery and Expression Analysis of Alternative Splicing Events Conserved among Plant SR Proteins

Cited by 39 publications

References 40 publications

Evolutionarily Conserved Alternative Splicing Across Monocots

Evolutionarily Conserved Alternative Splicing Across Monocots

A Comprehensive Analysis of Alternative Splicing in Paleopolyploid Maize

Identified of a novel cis-element regulating the alternative splicing of LcDREB2

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