Alternative Splicing Substantially Diversifies the Transcriptome during Early Photomorphogenesis and Correlates with the Energy Availability in Arabidopsis.
Plants use light as source of energy and information to detect diurnal rhythms and seasonal changes. Sensing changing light conditions is critical to adjust plant metabolism and to initiate developmental transitions. Here, we analyzed transcriptome-wide alterations in gene expression and alternative splicing (AS) of etiolated seedlings undergoing photomorphogenesis upon exposure to blue, red, or white light. Our analysis revealed massive transcriptome reprogramming as reflected by differential expression of ∼20% of all genes and changes in several hundred AS events. For more than 60% of all regulated AS events, light promoted the production of a presumably protein-coding variant at the expense of an mRNA with nonsense-mediated decay-triggering features. Accordingly, AS of the putative splicing factor REDUCED RED-LIGHT RESPONSES IN CRY1CRY2 BACKGROUND1, previously identified as a red light signaling component, was shifted to the functional variant under light. Downstream analyses of candidate AS events pointed at a role of photoreceptor signaling only in monochromatic but not in white light. Furthermore, we demonstrated similar AS changes upon light exposure and exogenous sugar supply, with a critical involvement of kinase signaling. We propose that AS is an integration point of signaling pathways that sense and transmit information regarding the energy availability in plants.
Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076 Tübingen, Germany.
Lisa
0000-0003-3494-2269
L
Hartmann
Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, New York 10065.|Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13092 Berlin, Germany.
Philipp
P
Drewe-Boß
Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076 Tübingen, Germany.
Theresa
T
Wießner
Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076 Tübingen, Germany.
Gabriele
G
Wagner
Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076 Tübingen, Germany.
Sascha
S
Geue
Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076 Tübingen, Germany.
Hsin-Chieh
HC
Lee
Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076 Tübingen, Germany.
Dominik M
DM
Obermüller
Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, New York 10065.
André
A
Kahles
Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, New York 10065.
Jonas
0000-0002-1288-1322
J
Behr
Institute for Neurobiology, University of Tübingen, 72076 Tübingen, Germany.
Fabian H
0000-0002-1348-9736
FH
Sinz
Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, New York 10065.|Department of Computer Science, ETH Zürich, 8006 Zürich, Switzerland.
Gunnar
G
Rätsch
Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076 Tübingen, Germany awachter@zmbp.uni-tuebingen.de.
Andreas
0000-0002-3132-5161
A
Wachter
D017398:Alternative Splicing / Q000235:genetics / Q000502:physiology*; D017360:Arabidopsis / Q000235:genetics* / Q000502:physiology; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D018506:Gene Expression Regulation, Plant / Q000235:genetics / Q000502:physiology; D015398:Signal Transduction / Q000235:genetics / Q000502:physiology; D059467:Transcriptome / Q000235:genetics*
D029681:Arabidopsis Proteins