Genome-wide mapping of alternative splicing in Arabidopsis thaliana

Abstract

Alternative splicing can enhance transcriptome plasticity and proteome diversity. In plants, alternative splicing can be manifested at different developmental stages, and is frequently associated with specific tissue types or environmental conditions such as abiotic stress. We mapped the Arabidopsis transcriptome at single-base resolution using the Illumina platform for ultrahigh-throughput RNA sequencing (RNA-seq). Deep transcriptome sequencing confirmed a majority of annotated introns and identified thousands of novel alternatively spliced mRNA isoforms. Our analysis suggests that at least ;42% of intron-containing genes in Arabidopsis are alternatively spliced; this is significantly higher than previous estimates based on cDNA/expressed sequence tag sequencing. Random validation confirmed that novel splice isoforms empirically predicted by RNA-seq can be detected in vivo. Novel introns detected by RNA-seq were substantially enriched in nonconsensus terminal dinucleotide splice signals. Alternative isoforms with premature termination codons (PTCs) comprised the majority of alternatively spliced transcripts. Using an example of an essential circadian clock gene, we show that intron retention can generate relatively abundant PTC + isoforms and that this specific event is highly conserved among diverse plant species. Alternatively spliced PTC + isoforms can be potentially targeted for degradation by the nonsense mediated mRNA decay (NMD) surveillance machinery or regulate the level of functional transcripts by the mechanism of regulated unproductive splicing and translation (RUST). We demonstrate that the relative ratios of the PTC + and reference isoforms for several key regulatory genes can be considerably shifted under abiotic stress treatments. Taken together, our results suggest that like in animals, NMD and RUST may be widespread in plants and may play important roles in regulating gene expression.[Supplemental material is available online at

The Differential Transcription Network between Embryo and Endosperm in the Early Developing Maize Seed

“…Retained intron, in which a single intron is alternatively included or spliced out of the mature mRNA via an intron-definition splicing mechanism, was the most prevalent type of AS event (30.4%; Fig. 3C), consistent with previous studies in plants (Black, 2003;Wang and Brendel, 2006;Barbazuk et al, 2008;Filichkin et al, 2010;Li et al, 2010;Lu et al, 2010;Zhang et al, 2010;Marquez et al, 2012) but in contrast to animal AS events, where exon skipping (cassette exons or coordinate cassette exons) is the predominant mechanism (Sultan et al, 2008;Wang et al, 2008;Daines et al, 2011;Graveley et al, 2011). Furthermore, alternative 39 splice sites (A3SS; 21.0%) or alternative last exons (ALE; 11.5%) and alternative 59 splice sites (A5SS; 12.2%) or alternative first exons (AFE; 11.7%) were other types of common AS events observed in our data (Fig.…”

“…For example, the Arabidopsis TF gene IDD14 generates two splicing variants to competitively form nonfunctional heterodimers to regulate starch metabolism (Seo et al, 2011). In our RNA-seq data of maize embryo and endosperm, 50.7% of multiexonic genes were found to undergo AS, which is higher than that in Arabidopsis and rice (Filichkin et al, 2010;Lu et al, 2010). This indicates that the splicing diversity of the maize transcriptome is more complex than that in Arabidopsis and rice.…”

“…It was reported that at least 42% and 48% of genes are alternatively spliced in Arabidopsis and rice, respectively (Filichkin et al, 2010;Lu et al, 2010).…”

“…RNA-seq data are highly reproducible, with few systematic discrepancies among technical replicates (Marioni et al, 2008). RNA-seq technology has been applied to uncovering the entire transcriptome and identifying alternative splicing (AS) and novel transcribed regions (NTRs) as well as chimeric transcripts produced by trans-splicing in human, yeast, mouse, Arabidopsis, and rice (Oryza sativa; Cloonan et al, 2008;Lister et al, 2008;Mortazavi et al, 2008;Nagalakshmi et al, 2008;Pan et al, 2008;Sultan et al, 2008;Wang et al, 2008;Wilhelm et al, 2008;Filichkin et al, 2010;Lu et al, 2010;Zhang et al, 2010).…”

One Gene, Many Proteins: Mapping Cell-Specific Alternative Splicing in Plants

“…Instead, Li et al (2016) observed that intron retention is the major type of AS in root tissues (>41%), in agreement with previous findings (Filichkin et al, 2010), followed by alternative acceptor (<26%) and alternative donor (>12%) splicing variants. The authors classified intron retention events as either type I (where the major isoform excises the intron) or type II (where the major isoform retains the intron).…”