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Proc Natl Acad Sci U S A. 2014 Dec 30;111(52):18781-6. doi: 10.1073/pnas.1407147112. Epub 2014 Dec 15.

Phytochrome controls alternative splicing to mediate light responses in Arabidopsis.

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Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan;
Frontier Research Academy for Young Researchers, Kyushu Institute of Technology, Fukuoka 820-8502, Japan;
Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan; and.
Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan; PRESTO, JST, Saitama 332-0012, Japan


Plants monitor the ambient light conditions using several informational photoreceptors, including red/far-red light absorbing phytochrome. Phytochrome is widely believed to regulate the transcription of light-responsive genes by modulating the activity of several transcription factors. Here we provide evidence that phytochrome significantly changes alternative splicing (AS) profiles at the genomic level in Arabidopsis, to approximately the same degree as it affects steady-state transcript levels. mRNA sequencing analysis revealed that 1,505 and 1,678 genes underwent changes in their AS and steady-state transcript level profiles, respectively, within 1 h of red light exposure in a phytochrome-dependent manner. Furthermore, we show that splicing factor genes were the main early targets of AS control by phytochrome, whereas transcription factor genes were the primary direct targets of phytochrome-mediated transcriptional regulation. We experimentally validated phytochrome-induced changes in the AS of genes that are involved in RNA splicing, phytochrome signaling, the circadian clock, and photosynthesis. Moreover, we show that phytochrome-induced AS changes of SPA1-RELATED 3, the negative regulator of light signaling, physiologically contributed to promoting photomorphogenesis. Finally, photophysiological experiments demonstrated that phytochrome transduces the signal from its photosensory domain to induce light-dependent AS alterations in the nucleus. Taking these data together, we show that phytochrome directly induces AS cascades in parallel with transcriptional cascades to mediate light responses in Arabidopsis.


alternative splicing; light signaling; photomorphogenesis; phytochrome; posttranscriptional regulation

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