Function of photobodies in Arabidopsis photoreceptor signaling

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Abstract How the cell nucleus is functionally and dynamically organized is a central question to understanding basic cellular processes, including genome organization and transcriptional regulation. The interphase of both animal and plant nuclei contain morphologically distinct, non-membrane bound subnuclear organelles that are collectively called nuclear bodies. Although accumulating evidence suggests that nuclear bodies play important roles in gene regulation, and changes in the morphology and constitution of nuclear bodies have been associated with diseases, the precise function and regulatory mechanism of nuclear body biogenesis in transcriptional regulation remain poorly understood. One major challenge has been the lack of genetic models to delineate the functions of nuclear bodies in the context of transcriptional regulation by cell signaling. The long-term goal of the PI’s laboratory is to utilize the photobody – a subnuclear domain in Arabidopsis containing the photoreceptor phytochrome B (PHYB) – as a genetic model to elucidate the function of nuclear bodies in cell signaling and transcriptional regulation. The current data support the central hypothesis that photobodies are transcriptional regulatory foci wherein PHYB recruits transcription factors to regulate their stability as well as the activity of their target genes. This hypothesis has been formulated on the basis of the PI’s previous molecular genetic studies on two new light signaling components required for photobody biogenesis, named HMR and RCB, and on the preliminary results showing direct recruitment of individual genes to photobodies. Here the PI plans to test this central hypothesis by the following specific aims: (1) Determine the function of photobodies in regulating the stability of transcription factors; (2) Determine the role of RCB in the function and biogenesis of photobodies; (3) Determine the mechanism of spatial genome organization by photobodies. The proposed research is innovative, because it utilizes the photobody and photoreceptor signaling in Arabidopsis as a genetic model to investigate the enigmatic mechanisms of nuclear organization – the function and biogenesis of nuclear bodies in transcriptional regulation and genome organization. The PI’s laboratory pioneered the development of the photobody model, identified new signaling components required for photobody formation by multiple forward genetic screens, and established a mechanistic link between photobodies and transcriptional regulation. The proposed research is significant because it is expected to uncover novel mechanisms linking nuclear body biogenesis to the regulation of the stability of transcription factors as well as the activity of their target genes. Because the basic principles of gene regulation are conserved across the animal, fungal, and plant kingdoms, a better understanding of the function of photobodies in Arabidopsis will contribute to understanding of the evolutionarily conserved principles of genome organization and transcriptional regulation in eukaryotes and thereby will ultimately enhance our understanding of the misregulation of nuclear organization in human diseases.