New pre-print from the lab: Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions highlight major functional differences with animals. Great collaboration with Paula Duque's lab @IGCiencia! @CRGenomica. https://biorxiv.org/cgi/content/short/2020.11.10.374751v1. Summary1/11

We have assembled a large resource of steady state mRNA levels (GE) and alternative splicing (AS) patterns for A. thaliana for multiple developmental time courses and adult tissues as well as abiotic and biotic stress, light conditions, and mutants for splicing regulators. 2/11

We found high levels of AS in A. thaliana, similar to those of Drosophila fruitflies (60-70% of multiexonic genes). As previously reported, intron retention is globally the most common type of AS, and exon skipping is much less prevalent than in animals. 3/11

However, non-intron retention events are overrepresented among most regulated AS sets we defined, indicating that the functional importance of these events in plants may have been underrated. 4/11

On the regulatory side, reduction in core spliceosomal activity seems to be at least in part behind the AS response to abiotic stress in A. thaliana, providing a plausible explanation for the hypersensitivity of many splicing factor mutants to abiotic stresses. 5/11

On the functional side, AS regulated by abiotic and biotic stress as well as across tissues are significantly enriched - for all AS types - in potentially regulatory events (i.e. not giving rise to alternative protein isoforms). 6/11

Among them, we found a molecular signature of stress-regulated AS events modulating the 5' UTR sequence of genes harboring upstream open reading frames (uORFs). 7/11

Despite this role of AS regulating functional mRNA levels, genes differentially regulated by AS or GE under different conditions do not significantly overlap (as shown by many others before). I.e. they are largely independent and complementary regulatory layers. 8/11

Indeed, these separate regulatory layers seem genomically hardwired: genes that exhibit predominantly transcriptional or post-transcriptional control have mutually exclusive genomic features. And these differential patterns were also observed for their master regulators. 9/11

Finally, we performed a direct comparison with three animal models, using equivalent datasets. Interestingly, plants exhibit a much higher relative contribution of AS to stress responses respect to tissue diversification compared to animals. 10/11

And, of course, you can find all these data in PastDB ( http://pastdb.crg.eu ), the plant sister of @VastDB! 11/11