Genome-wide mapping of alternative splicing in Arabidopsis thaliana.

By S. Filichkin, Henry D. Priest, Scott A. Givan, Rongkun Shen, Doug Bryant, Samuel E. Fox, Weng-Keen Wong, Todd C. Mockler. Genome Research, 2010

917 citations recorded by the source corpus.

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 approximately 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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/5949869823c3fa4bb6bd492feb223c62e86fb54c

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools (2011, methodology): “Data used for this release included a total of 538 million reads obtained from two groups (28,35).”
Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis (2012, methodology): “The most recent estimate based on RNA-seq is that ;42% of Arabidopsis intron-containing genes undergo AS (Filichkin et al. 2010).”
Complexity of the Alternative Splicing Landscape in Plants[C][W][OPEN] (2013, methodology): “Accordingly,basedon EST and RNA-seq analyses of wild-type plants, 36 to 78% of Arabidopsis AS transcripts have been estimated to be potential candidates for NMD (Wang and Brendel, 2006; Filichkin et al., 2010).”
The developmental dynamics of the maize leaf transcriptome (2010, background): “We detected a gradient of gene expression from base to tip: basal (23,354) >transitional (22,663) >maturing (22,036) >mature (21,332).”
Alternative Splicing at the Intersection of Biological Timing, Development, and Stress Responses[OPEN] (2013, background): “…SR proteins that are key regulators of AS undergo AS themselves in response to extreme temperatures (Lazar and Goodman, 2000; Palusa et al., 2007; Filichkin et al., 2010) and other stresses, such as salt stress (Palusa et al., 2007; Tanabe et al., 2007) and highlight stress (Tanabe et al., 2007;…”