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Chromatin analysis of an Arabidopsis Phytochrome A allele reveals the correlation of transcriptional repression with recalcitrance to histone acetylation

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Abstract

Phytochrome A (phyA) is a major photoreceptor of red light that regulates seedling de-etiolation. The wild-type PHYA is abundantly expressed in dark and repressed by light through chromatin modification involving histone hypoacetylation and enrichment of the repressive histone mark, H3 lysine 27 trimethylation (H3K27me3). Earlier, an Arabidopsis phyA allele, phyA-17, was reported that contains hypermethylation in the gene body, and is repressed constitutively (transcriptional repression in the dark). In this study, chromatin analysis of phyA-17 was done to understand the basis of its transcriptional repression. Specifically, this study analyzed four different histone modifications on phyA-17 and the wild-type PHYA (Columbia-0) in light and dark conditions. This analysis revealed hypoacetylation of phyA-17 chromatin in both conditions correlating with its constitutive repression. However, relative enrichment of H3K27me3 on phyA-17 chromatin was not detected in either condition. Histone hypoacetylation suggested a role of histone deacetylases in phyA-17 repression. Chemical inhibitors of histone deacetylases, Trichostatin A and Sodium Butyrate, induced partial de-etiolation of phyA-17 seedlings without activating the resident phyA gene. Gene expression analysis revealed activation of the phyA-signaling pathway by Trichostatin A, suggesting a role of histone deacetylases downstream in the seedling de-etiolation pathway. However, since phyA-17 repression is not dependent on histone deacetylases, recalcitrance to histone acetylation by histone acetyl transferases, possibly due to hypermethylation, is likely the basis of its hypoacetylated chromatin.

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Acknowledgments

This study was funded by the Arkansas Division of Agriculture, and Arkansas Bioscience Institute. Authors are grateful to Arabidopsis Biological Resource Center at The Ohio State University for providing phyA-211, hda9 (SALK_007123), hda15 (SALK_004027C), and hda19 (SALK_139445) seeds.

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Authors and Affiliations

  1. Department of Crop, Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA

    Gulab Rangani, Jamie L. Underwood & Vibha Srivastava

  2. Department of Horticulture, University of Arkansas, Fayetteville, AR, 72701, USA

    Vibha Srivastava

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  1. Gulab Rangani
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  2. Jamie L. Underwood
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Correspondence to Vibha Srivastava.

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Rangani, G., Underwood, J.L. & Srivastava, V. Chromatin analysis of an Arabidopsis Phytochrome A allele reveals the correlation of transcriptional repression with recalcitrance to histone acetylation. Plant Growth Regul 75, 179–186 (2015). https://doi.org/10.1007/s10725-014-9942-8

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  • DOI: https://doi.org/10.1007/s10725-014-9942-8

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