Comprehensive discovery of salt-responsive alternative splicing events based on Iso-Seq and RNA-seq in grapevine roots

Jin, Zhongxin; Lv, Xinning; Sun, Yushuai; Fan, Zongbao; Xiang, Guangqing; Yao, Yuxin

doi:10.1016/j.envexpbot.2021.104645

Cited by 10 publications

(7 citation statements)

References 63 publications

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“…Finally, the prevalent AS event type observed in Z. japonica under cold and salt stress conditions was the retained intron (RI) type. This observation aligns with findings from prior investigations in other plant species such as Arabidopsis (Ner‐Gaon et al, 2004), apple, orange, strawberry, pineapple (Sablok et al, 2017) and grape (Jin et al, 2021). The RI type of AS event involves the retention of intronic sequences in mature mRNA, potentially enhancing the functional diversity of encoded proteins.…”

Section: Discussionsupporting

confidence: 91%

Unveiling unique alternative splicing responses to low temperature in Zoysia japonica through ZjRTD1.0, a high‐quality reference transcript dataset

Wu,

He,

Wang

et al. 2024

Physiologia Plantarum

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Inadequate reference databases in RNA‐seq analysis can hinder data utilization and interpretation. In this study, we have successfully constructed a high‐quality reference transcript dataset, ZjRTD1.0, for Zoysia japonica, a widely‐used turfgrass with exceptional tolerance to various abiotic stress, including low temperatures and salinity. This dataset comprises 113,089 transcripts from 57,143 genes. BUSCO analysis demonstrates exceptional completeness (92.4%) in ZjRTD1.0, with reduced proportions of fragmented (3.3%) and missing (4.3%) orthologs compared to prior datasets. ZjRTD1.0 enables more precise analyses, including transcript quantification and alternative splicing assessments using public datasets, which identified a substantial number of differentially expressed transcripts (DETs) and differential alternative splicing (DAS) events, leading to several novel findings on Z. japonica's responses to abiotic stresses. First, spliceosome gene expression influenced alternative splicing significantly under abiotic stress, with a greater impact observed during low‐temperature stress. Then, a significant positive correlation was found between the number of differentially expressed genes (DEGs) encoding protein kinases and the frequency of DAS events, suggesting the role of protein phosphorylation in regulating alternative splicing. Additionally, our results suggest possible involvement of serine/arginine‐rich (SR) proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs) in generating inclusion/exclusion isoforms under low‐temperature stress. Furthermore, our investigation revealed a significantly enhanced overlap between DEGs and differentially alternatively spliced genes (DASGs) in response to low‐temperature stress, suggesting a unique co‐regulatory mechanism governing transcription and splicing in the context of low‐temperature response. In conclusion, we have proven that ZjRTD1.0 will serve as a reliable and useful resource for future transcriptomic analyses in Z. japonica.

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Section: Discussionsupporting

confidence: 91%

Unveiling unique alternative splicing responses to low temperature in Zoysia japonica through ZjRTD1.0, a high‐quality reference transcript dataset

Wu,

He,

Wang

et al. 2024

Physiologia Plantarum

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“…qPCR quantification of the primary transcripts provides further evidence for the parallel role of AS in stress responses. Similar patterns were obtained in other plant species in a variety of interactions under conditions of salt stress in grapevine (Jin et al, 2021), heat stress in Physcomitrella patens (Chang et al, 2014), cold stress in Cassava (Li et al, 2020), and insect herbivory in Nicotiana attenuata (Chang et al, 2014; Li et al, 2013; Ling et al, 2015; Liu et al, 2018).…”

Section: Discussionsupporting

confidence: 72%

“…These elements typically control AS by identifying the cis-elements in exons or introns and regulating the spliceosome complex assembly at the adjacent splice sites. Previous reports have indicated that these SFs are intensely governed by various stressors (Jin et al, 2021;Li et al, 2020). Precise investigation of the changes in the transcript levels of SFs offers some insights since they play a significant role in constitutive and AS.…”

Section: Qpcr Validation Of Mymiv-responsive Das Isoforms and Their P...mentioning

confidence: 99%

Deciphering the role of alternative splicing as modulators of defense response in the MYMIV–Vigna mungo pathosystem

Laskar

Hazra

Pal

et al. 2023

Physiologia Plantarum

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Alternative splicing (AS) is a crucial regulatory mechanism that impacts transcriptome and proteome complexity under stressful situations. Although its role in abiotic stresses is somewhat understood, our understanding of the mechanistic regulation of pre‐messenger RNA splicing in plant‐pathogen interaction is meager. To comprehend this unexplored immune reprogramming mechanism, transcriptome profiles of Mungbean Yellow Mosaic India Virus (MYMIV)‐resistant and susceptible Vigna mungo genotypes were analyzed for AS genes that may underlie the resistance mechanism. Results revealed a repertoire of AS‐isoforms accumulated during pathogenic infestation, with intron retention being the most common AS mechanism. Identification of 688 differential alternatively spliced (DAS) genes in the resistant host elucidates its robust antiviral response, whereas 322 DAS genes were identified in the susceptible host. Enrichment analyses confirmed DAS transcripts pertaining to stress, signaling, and immune system pathways have undergone maximal perturbations. Additionally, a strong regulation of the splicing factors has been observed both at the transcriptional and post‐transcriptional levels. qPCR validation of candidate DAS transcripts with induced expression upon MYMIV infection demonstrated a competent immune response in the resistant background. The AS‐impacted genes resulted either in partial/complete loss of functional domains or altered sensitivity to micro‐RNA‐mediated gene silencing. A complex regulatory module, miR7517‐ATAF2, has been identified in an aberrantly spliced ATAF2 isoform that exposes an intronic miR7517 binding site, thereby suppressing the negative regulator to enhance the defense reaction. The present study establishes AS as a noncanonical immune reprogramming mechanism that operates in parallel, thereby offering an alternative strategy for developing yellow mosaic‐resistant V. mungo cultivars.

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“…Pioneering work performed by Anvar et al, (2018) based on Iso-Seq data uncovered widespread coupling between transcription initiation and mRNA processing in MCF-7 breast cancer cells; this research was based on the detection principle where exons serve as the basic units, which facilitates the discovery of linked exons but makes it di cult to describe AS events, especially for events with overlapping exons such as A3 and A5. To identify AS event-related interactions, we initially tried to integrate AStalavista into the analysis process of interdependency in our previous study (Jin et al, 2021); AStalavista decides AS events by non xed number of exons and produced extremely diverse AS events (Foissac and Sammeth, 2007); however, these overly complex results are often unnecessary and could be detrimental to the discovery of common AS types. SUPPA2 de nes AS events based on anking exons, introns and alternative cassette exons and produces several common and understandable AS types (Trincado et al, 2018) and thus was integrated into the ASAPA pipeline (Fig.…”

Section: Discussionmentioning

confidence: 99%

ASAPA: a bioinformatic pipeline based on Iso-Seq that identifies the links among alternative splicing, alternative transcription initiation and alternative polyadenylation

Wang,

Jin,

Wang

et al. 2024

Funct Integr Genomics

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Background: Although the events associated with alternative splicing (AS), alternative polyadenylation (APA) and alternative transcription initiation (ATI) can be identi ed by many approaches based on isoform sequencing (Iso-Seq), these analyses are generally independent of each other and the links between these events are still rarely mentioned. However, an interdependency analysis can be achieved because the transcriptional start site, splice sites and polyA site could be simultaneously included in a long, full-length read from Iso-Seq.Results: We create ASAPA pipeline that enables streamlined analysis for a robust detection of potential links among AS, ATI and APA using Iso-Seq data. We tested this pipeline using Arabidopsis data and found some interesting results: some adjacent introns tend to be simultaneously spliced or retained; coupling between AS and ATI or APA is limited to the initial or terminal intron; and ATI and APA are potentially linked in some special cases. Conclusion: Our pipeline enables streamlined analysis for a robust detection of potential links among AS, ATI and APA using Iso-Seq data, which is conducive to a better understanding of transcription landscape generation.

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Comprehensive discovery of salt-responsive alternative splicing events based on Iso-Seq and RNA-seq in grapevine roots

Cited by 10 publications

References 63 publications

Unveiling unique alternative splicing responses to low temperature in Zoysia japonica through ZjRTD1.0, a high‐quality reference transcript dataset

Unveiling unique alternative splicing responses to low temperature in Zoysia japonica through ZjRTD1.0, a high‐quality reference transcript dataset

Deciphering the role of alternative splicing as modulators of defense response in the MYMIV–Vigna mungo pathosystem

ASAPA: a bioinformatic pipeline based on Iso-Seq that identifies the links among alternative splicing, alternative transcription initiation and alternative polyadenylation

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