Phytochrome controls alternative splicing to mediate light responses in Arabidopsis

Hiromasa Shikata, Kousuke Hanada, Tomokazu Ushijima, Moeko Nakashima, Yutaka Suzuki, Tomonao Matsushita

Research output: Contribution to journalArticle

65 Citations (Scopus)

Abstract

Plantsmonitor 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.

Original languageEnglish
Pages (from-to)18781-18786
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume111
Issue number52
DOIs
Publication statusPublished - Dec 30 2014

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Phytochrome
Alternative Splicing
Arabidopsis
Light
Genes
Transcription Factors
RNA Splicing
Circadian Clocks
Photosynthesis

All Science Journal Classification (ASJC) codes

  • General

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Phytochrome controls alternative splicing to mediate light responses in Arabidopsis. / Shikata, Hiromasa; Hanada, Kousuke; Ushijima, Tomokazu; Nakashima, Moeko; Suzuki, Yutaka; Matsushita, Tomonao.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 111, No. 52, 30.12.2014, p. 18781-18786.

Research output: Contribution to journalArticle

Shikata, Hiromasa ; Hanada, Kousuke ; Ushijima, Tomokazu ; Nakashima, Moeko ; Suzuki, Yutaka ; Matsushita, Tomonao. / Phytochrome controls alternative splicing to mediate light responses in Arabidopsis. In: Proceedings of the National Academy of Sciences of the United States of America. 2014 ; Vol. 111, No. 52. pp. 18781-18786.
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