Abstract
Plants in the natural environment experience continuous dynamic changes in light intensity. Here, we exposed Arabidopsis thaliana plants to naturally fluctuating light (FL) regimes alongside traditional square light (SQ) regimes such as those often found in control environment growth chambers. The physiological response was highly consistent across experiments in sibling plants, indicating the possibility of an epigenetic mechanism, leading us to investigate differences in DNA methylation. Our results identified a large number of changes in DNA methylation patterns between FL-acclimated plants and SQ-acclimated plants, demonstrating that natural fluctuations in light impact plant epigenetic mechanisms. Most importantly, there are more differences in DNA methylation patterns between different light pattern regimes than between different light intensities. These differences in DNA methylation were accompanied by significant changes in gene expression, some of which correlated with altered DNA methylation. One of these genes, MCCA, was found to significantly impact photosynthetic efficiency when knocked out. Thousands of transposable element (TE) copies were differentially methylated between light regimes. Interestingly, up to 30% of these TEs are linked to nearby differentially expressed genes. Our data suggest DNA methylation plays a role in acclimation to natural light, which may directly regulate gene expression and impact TE activation.
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Claims 7
Claim · model-written summary
Sibling Arabidopsis plants showed highly consistent physiological responses across experiments.
- Taxon
- Arabidopsis thaliana
Arabidopsis thalianae1 - Outcome
- physiological responsee0
- Direction
- highly consistente0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The physiological response was highly consistent across experiments in sibling plants”
e1“Arabidopsis thaliana plants”
Claim · model-written summary
Fluctuating and square light regimes produced many differences in DNA methylation patterns.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae1
- Treatment
- FL-acclimated plantse0
- Outcome
- DNA methylation patternse0
- Direction
- changese0
- Comparator
- SQ-acclimated plantse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“a large number of changes in DNA methylation patterns between FL-acclimated plants and SQ-acclimated plants”
e1“Arabidopsis thaliana plants”
Claim · model-written summary
Light pattern regimes yielded more methylation differences than light intensities.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae1
- Treatment
- different light pattern regimese0
- Outcome
- differences in DNA methylation patternse0
- Direction
- moree0
- Comparator
- different light intensitiese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“more differences in DNA methylation patterns between different light pattern regimes than between different light intensities”
e1“Arabidopsis thaliana plants”
Claim · model-written summary
Methylation differences accompanied significant gene expression changes, some correlated with methylation.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae1
- Treatment
- differences in DNA methylatione0
- Outcome
- changes in gene expressione0
- Qualifier
- some of which correlated with altered DNA methylatione0
Not reportedCompoundDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“These differences in DNA methylation were accompanied by significant changes in gene expression, some of which correlated with altered DNA methylation”
e1“Arabidopsis thaliana plants”
Claim · model-written summary
MCCA knockout significantly affected photosynthetic efficiency.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae1
- Treatment
- knocked oute0
- Gene
- MCCAe0
- Outcome
- photosynthetic efficiencye0
Not reportedComparatorDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“MCCA, was found to significantly impact photosynthetic efficiency when knocked out”
e1“Arabidopsis thaliana plants”
Claim · model-written summary
Thousands of transposable element copies were differentially methylated between light regimes.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae1
- Outcome
- transposable element (TE) copies were differentially methylatede0
- Direction
- differentially methylatede0
- Qualifier
- between light regimese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Thousands of transposable element (TE) copies were differentially methylated between light regimes”
e1“Arabidopsis thaliana plants”
Claim · model-written summary
Up to 30% of differentially methylated transposable elements were linked to nearby differentially expressed genes.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae1
- Gene
- nearby differentially expressed genese0
- Outcome
- these TEs are linkede0
- Value
- up to 30%e0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“up to 30% of these TEs are linked to nearby differentially expressed genes”
e1“Arabidopsis thaliana plants”