Computational analysis of alternative splicing in plant genomes

Song, Qi; Catlin, Nathan S.; Barbazuk, W. Brad; Song, Li

doi:10.1016/j.gene.2018.10.026

Cited by 12 publications

(8 citation statements)

References 118 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…It is now accepted that increased sequencing depth, together with the consideration of multiple reads from replicate samples covering a splice junction, allow for improving the accuracy of AS event detection. We used the rMATS software, shown effective in plants for accurate AS analysis from replicate data [ 37 ], to analyze and statistically validate the differential events occurring between two conditions, either consecutive stages, or the two varieties at each stage. Thereafter, we applied stringent threshold values for the number of reads covering the splice junction and for the ratio of splice isoforms (ILs), in order to select only the most reliable results.…”

Section: Discussionmentioning

confidence: 99%

“…In addition, we statistically analysed the difference in gene AS between the two varieties at the different stages. The comparisons were performed using the software rMATS (replicate Multivariate-Analysis-of-Transcript-Splicing), primarily designed for AS analysis from replicate human samples [ 36 ], and that has recently been shown to be effective for accurate detection of differential AS (DAS) events in plant species [ 37 ].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Alternative splicing regulation appears to play a crucial role in grape berry development and is also potentially involved in adaptation responses to the environment

et al. 2021

View full text Add to dashboard Cite

Background Alternative splicing (AS) produces transcript variants playing potential roles in proteome diversification and gene expression regulation. AS modulation is thus essential to respond to developmental and environmental stimuli. In grapevine, a better understanding of berry development is crucial for implementing breeding and viticultural strategies allowing adaptation to climate changes. Although profound changes in gene transcription have been shown to occur in the course of berry ripening, no detailed study on splicing modifications during this period has been published so far. We report here on the regulation of gene AS in developing berries of two grapevine (Vitis vinifera L.) varieties, Gewurztraminer (Gw) and Riesling (Ri), showing distinctive phenotypic characteristics. Using the software rMATS, the transcriptomes of berries at four developmental steps, from the green stage to mid-ripening, were analysed in pairwise comparisons between stages and varieties. Results A total of 305 differential AS (DAS) events, affecting 258 genes, were identified. Interestingly, 22% of these AS events had not been reported before. Among the 80 genes that underwent the most significant variations during ripening, 22 showed a similar splicing profile in Gw and Ri, which suggests their involvement in berry development. Conversely, 23 genes were subjected to splicing regulation in only one variety. In addition, the ratios of alternative isoforms were different in Gw and Ri for 35 other genes, without any change during ripening. This last result indicates substantial AS differences between the two varieties. Remarkably, 8 AS events were specific to one variety, due to the lack of a splice site in the other variety. Furthermore, the transcription rates of the genes affected by stage-dependent splicing regulation were mostly unchanged, identifying AS modulation as an independent way of shaping the transcriptome. Conclusions The analysis of AS profiles in grapevine varieties with contrasting phenotypes revealed some similarity in the regulation of several genes with developmental functions, suggesting their involvement in berry ripening. Additionally, many splicing differences were discovered between the two varieties, that could be linked to phenotypic specificities and distinct adaptive capacities. Together, these findings open perspectives for a better understanding of berry development and for the selection of grapevine genotypes adapted to climate change.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Alternative splicing regulation appears to play a crucial role in grape berry development and is also potentially involved in adaptation responses to the environment

et al. 2021

View full text Add to dashboard Cite

show abstract

“…AS is a process occurring in all higher eukaryotes whereby the same precursor mRNA generates multiple transcripts with variable quantities. AS is a major mechanism to achieve proteomic diversity with de ned gene numbers (Ast 2004;Nilsen and Graveley 2010;Song et al 2019). In human, more than 95% of multiexonic genes are alternatively spliced (Syed et al 2012).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Differences in Gene Expression and Alternative Splicing in Developing Embryo and Endosperm, and Between F1 Hybrids and Their Parental Pure Lines in Sorghum

Zhang

Yang

et al. 2021

Preprint

View full text Add to dashboard Cite

Differential regulation of gene expression and alternative splicing (AS) are major molecular mechanisms dictating plant growth and development, as well as underpinning heterosis in F1 hybrids. Here, using deep RNA-sequencing we analyzed differences in genome-wide gene expression and AS between developing embryo and endosperm, and between F1 hybrids and their pure-line parents in sorghum. We uncover dramatic differences in both gene expression and AS between embryo and endosperm with respect to gene features and functions, which are consistent with the fundamentally different biological roles of the two tissues. Accordingly, F1 hybrids showed substantial and multifaceted differences in gene expression and AS compared with their pure-line parents, again with clear tissue specificities including extents of difference, genes involved and functional enrichments. Our results provide useful transcriptome resources as well as novel insights for further elucidation of seed yield heterosis in sorghum and related crops.

show abstract

“…Current approaches to analyse splicing involve exploration of the transcriptome with nextgeneration sequencing, still mostly with short-read RNA-seq data 4,5,16,17 . These approaches rely on mapping the short-read sequences to the gene and subsequently take two distinct strategies.…”

Section: Introductionmentioning

confidence: 99%

Splice-site Strength Estimation: A simple yet powerful approach to analyse RNA splicing

Dent¹,

Singh²,

Mishra

et al. 2020

Preprint

View full text Add to dashboard Cite

Association Studies.RNA splicing, and variations in this process referred to as alternative splicing, are critical aspects of gene regulation in eukaryotes. From environmental responses in plants to being a primary link between genetic variation and disease in humans, splicing differences confer extensive phenotypic changes across diverse organisms 1-3 . Current approaches for analysing splicing rely on quantifying variant transcripts (i.e., isoforms) or splicing events (i.e., intron retention, exon skipping etc) 4,5 . However, regulation of splicing occurs at the level of selection of individual splice sites, which results in variation in the abundance of isoforms and/or splicing events. Here, we present a simple approach to quantify the strength of individual splice sites, which determines their selection in a splicing reaction.Splice-site strength, as a quantitative phenotype, allows us to analyse splicing precisely in unprecedented ways. We demonstrate the power of this approach in defining the genomic determinants of the strength of individual splice-sites through GWAS. Our pilot-GWAS with more than thousand splice sites hints that cis-sequence divergence and competition between splice-sites and are among the primary determinants of variation in splicing among natural accessions of Arabidopsis thaliana. This approach allows deciphering the principles of splicing, which in turn has implications that range from agriculture to medicine.

show abstract

Computational analysis of alternative splicing in plant genomes

Cited by 12 publications

References 118 publications

Alternative splicing regulation appears to play a crucial role in grape berry development and is also potentially involved in adaptation responses to the environment

Alternative splicing regulation appears to play a crucial role in grape berry development and is also potentially involved in adaptation responses to the environment

Genome-Wide Differences in Gene Expression and Alternative Splicing in Developing Embryo and Endosperm, and Between F1 Hybrids and Their Parental Pure Lines in Sorghum

Splice-site Strength Estimation: A simple yet powerful approach to analyse RNA splicing

Contact Info

Product

Resources

About