Acute Effects of Light on Alternative Splicing in Light‐Grown Plants

Abstract

Light modulates plant growth and development to a great extent by regulating gene expression programs. Here, we evaluated the effect of light on alternative splicing (AS) in light-grown Arabidopsis thaliana plants using high-throughput RNA sequencing (RNA-seq). We found that an acute light pulse given in the middle of the night, a treatment that simulates photoperiod lengthening, affected AS events corresponding to 382 genes. Some of these AS events were associated with genes involved in primary metabolism and stress responses, which may help to adjust metabolic and physiological responses to seasonal changes. We also found that several core clock genes showed changes in AS in response to the light treatment, suggesting that light regulation of AS may play a role in clock entrainment. Finally, we found that many light-regulated AS events were associated with genes encoding RNA processing proteins and splicing factors, supporting the idea that light regulates this posttranscriptional regulatory layer through AS regulation of splicing factors. Interestingly, the effect of a red-light pulse on AS of a gene encoding a splicing factor was not impaired in a quintuple phytochrome mutant, providing unequivocal evidence that nonphotosensory photoreceptors control AS in light-grown plants.

Alternative Splicing Substantially Diversifies the Transcriptome during Early Photomorphogenesis and Correlates with the Energy Availability in Arabidopsis

“…This observation is in line with previous studies showing extensive and regulated AS for the pre-mRNAs of many splicing factors (Reddy and Shad Ali, 2011;Syed et al, 2012;Wachter et al, 2012;Reddy et al, 2013;Staiger and Brown, 2013;Mancini et al, 2016), which allows quantitative gene control by coupling to NMD (see above) but might also increase their functional diversity. Interestingly, among our candidates was RRC1, a putative splicing factor that had previously been identified as a component of PHYB signaling (Shikata et al, 2012a;Shikata et al, 2012b showed that the C-terminal arginine/serine-rich (RS) domain of RRC1 is required for its function in PHYB signaling (Shikata et al, 2012a;Shikata et al, 2012b).…”

“…Comparisons of AS profiles for light-versus dark-grown rice seedlings using microarrays (Jung et al, 2009) and for A. thaliana seedlings with a high-resolution reverse transcription polymerase chain reaction (RT-PCR) panel (Simpson et al, 2008) indicated that light-mediated changes in AS patterns might affect the expression of numerous genes. This notion was further supported by recent studies using RNA sequencing (RNA-seq) to deduce light-regulated AS patterns in a transcriptome-wide manner in the moss Physcomitrella patens (Wu et al, 2014), etiolated A. thaliana seedlings (Shikata et al, 2014), and light-grown A. thaliana plants (Mancini et al, 2016). Interestingly, Wu et al (2014) and Shikata et al (2014) reported PHY signaling acting upstream of light-regulated AS.…”

“…Analysis of red-light responsive AS for a splicing factor gene in a phy quintuple mutant from A. thaliana also excluded, at least in light-grown plants, a role of the other PHYs in this process (Mancini et al, 2016). We observed that a contribution of PHYA/B to light-mediated AS is only detectable under red and far-red light.…”

“…Interestingly, Wu et al (2014) and Shikata et al (2014) reported PHY signaling acting upstream of light-regulated AS. By contrast, AS patterns for a subset of genes in A. thaliana exposed to alternating light/dark conditions changed independent of photoreceptors (Petrillo et al, 2014a;Petrillo et al, 2014b;Mancini et al, 2016). These findings raise the intriguing questions whether independent signaling pathways in light-regulated AS exist and how AS changes can contribute to plant adaptation to altered light conditions.…”

“…To gain a better understanding of light-triggered AS, the upstream regulatory components need to be identified. Two recent studies analyzing light-induced AS in P. patens (Wu et al, 2014) and etiolated A. thaliana seedlings (Shikata et al, 2014) shown to be independent of photoreceptors (Petrillo et al, 2014b;Mancini et al, 2016). Based on our data, the PHYA/B and CRY photoreceptors also play no major role in AS control during photomorphogenesis in normal light conditions.…”