Biology subjects

Loraine, A.

Publications and source records attributed to Loraine, A..

2 recordsLinked to original sources

bioRxiv2018

Cytokinin treatment of rice induces minimal effect on differential splicing compared to splicing between tissues

Alternatively spliced genes produce multiple spliced isoforms, called transcript variants. In differential alternative splicing, the relative abundance of transcript variants differs across sample types. Differential alternative splicing is common in animal systems and influences cellular development in many processes, but its extent and significance is not as well known in plants. To investigate alternative splicing in plants, we examined rice seedling RNA-Seq data that included approximately 40 million sequence alignments per library, three libraries per sample type, and four sample types: roots and shoots, each treated with exogenous cytokinin delivered hydroponically, plus mock-treated controls. Cytokinin treatment triggered expression changes in thousands of genes, but had minimal effect on alternative splicing. However, there were many splicing differences between roots and shoots. Analysis of a similar (but less deeply sequenced) mRNA-Seq data set from Arabidopsis showed the same pattern. Quantitative fragment analysis of reverse transcriptase-PCR products made from newly prepared rice samples confirmed nine of ten differential splicing events between rice roots and shoots. In both the Arabidopsis and rice mRNA-Seq data sets, most genes annotated as alternatively spliced had small minor variant frequencies, i.e., the less frequently observed forms were supported by fewer than 20% of informative mRNA-Seq sequences. Of splicing choices where there was more abundant support for minor forms, most alternative splicing events were located within the protein-coding sequence and also maintained the annotated reading frame. A tool for visualizing protein annotations in the context of genomic sequence (ProtAnnot) together with a genome browser (Integrated Genome Browser) were used to visualize and assess effects of differential splicing on gene function. In general, differentially spliced regions coincided with conserved regions in the encoded proteins, indicating that differential alternative splicing is likely to affect protein function between root and shoot tissue in rice.

molecular biology↗

bioRxiv2017

Genome-Wide Characterization Of Isoform Switching In Arabidopsis thaliana

SUMMARYAlternative splicing and the usage of alternate transcription start- or stop sites allows a single gene to produce multiple transcript isoforms. Most plant genes express one isoform at a significantly higher level than others, but under specific conditions this expression dominance can switch to different isoforms. These isoform switches have been observed for thousands of Zea mays and Vitis vinifera genes and have been linked to development and stress response. In Arabidopsis thaliana however, isoform switches have only been reported for 812 genes and the characteristics of these genes, nor the implications of the isoform switches on their protein functions, are currently well understood. Here we present a dataset of isoform dominance and switching for all genes in the AtRTD2 annotation based on a protocol that was benchmarked on simulated data and validated through comparison with a published RT-PCR panel. We report 138,722 isoform switches for 8,162 genes across 206 public RNA-Seq samples and find that these switches change the protein sequences in 23% of the cases. The observed isoform switches show high consistency across replicates and reveal reproducible patterns in response to treatment and development. We also demonstrate that genes with different ages, expression breadths, and functions show large differences in the frequency at which they switch isoforms and in the effect that these isoform switches have on their protein sequences. Finally, we showcase how the detected isoform switches can be applied to gain further insight in the regulation of a genes expression and function.\n\nSIGNIFICANCE STATEMENTIsoform switching through alternative splicing has been reported for thousands of genes in plants, yet genome-wide datasets to study the implications for gene functions are thus far not available. Here we present the first reference dataset of isoform dominance and switching for Arabidopsis thaliana based on 206 public RNA-Seq samples and provide novel insights in the regulation and functional consequences of alternative splicing.

plant biology↗