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.
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Claims 8
Claim · model-written summary
An acute light pulse given in the middle of the night affected alternative splicing events corresponding to 382 genes in Arabidopsis thaliana.
- Taxon
- Arabidopsis thaliana
Arabidopsis thalianae1 - Treatment
- an acute light pulse given in the middle of the nighte2
- Outcome
- AS eventse2
- Value
- 382 genese2
Not reportedComparatorDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“in light-grown Arabidopsis thaliana plants”
e2“an acute light pulse given in the middle of the night, a treatment that simulates photoperiod lengthening, affected AS events corresponding to 382 genes”
Claim · model-written summary
Some light-affected alternative splicing events were associated with genes involved in primary metabolism and stress responses.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae1
- Gene
- genes involved in primary metabolism and stress responsese3
- Outcome
- AS eventse3
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“in light-grown Arabidopsis thaliana plants”
e3“Some of these AS events were associated with genes involved in primary metabolism and stress responses”
Claim · model-written summary
A light treatment changed alternative splicing of several core clock genes.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae1
- Treatment
- light treatmente4
- Gene
- core clock genese4
- Outcome
- changes in ASe4
Not reportedComparatorDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“in light-grown Arabidopsis thaliana plants”
e4“several core clock genes showed changes in AS in response to the light treatment”
Claim · model-written summary
Light regulation of alternative splicing may play a role in clock entrainment.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae1
- Treatment
- light regulation of ASe5
- Outcome
- clock entrainmente5
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“in light-grown Arabidopsis thaliana plants”
e5“suggesting that light regulation of AS may play a role in clock entrainment”
Claim · model-written summary
Many light-regulated alternative splicing events were associated with genes encoding RNA processing proteins and splicing factors.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae1
- Gene
- genes encoding RNA processing proteins and splicing factorse6
- Outcome
- AS eventse6
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“in light-grown Arabidopsis thaliana plants”
e6“many light-regulated AS events were associated with genes encoding RNA processing proteins and splicing factors”
Claim · model-written summary
Light may regulate the posttranscriptional regulatory layer through alternative splicing regulation of splicing factors.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae1
- Gene
- splicing factorse7
- Outcome
- posttranscriptional regulatory layere7
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“in light-grown Arabidopsis thaliana plants”
e7“supporting the idea that light regulates this posttranscriptional regulatory layer through AS regulation of splicing factors”
Claim · model-written summary
A red-light pulse did not impair alternative splicing of a splicing-factor gene in a quintuple phytochrome mutant.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae1
- Material
- quintuple phytochrome mutante6
- Treatment
- a red-light pulsee6
- Gene
- a gene encoding a splicing factore6
- Outcome
- ASe6
- Direction
- not impairede6
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“in light-grown Arabidopsis thaliana plants”
e6“the effect of a red-light pulse on AS of a gene encoding a splicing factor was not impaired in a quintuple phytochrome mutant”
Claim · model-written summary
Nonphotosensory photoreceptors control alternative splicing in light-grown plants.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae1
- Outcome
- control ASe7
- Qualifier
- nonphotosensory photoreceptorse7
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“in light-grown Arabidopsis thaliana plants”
e7“providing unequivocal evidence that nonphotosensory photoreceptors control AS in light-grown plants”