Meta-Analysis of the Transcriptome Reveals a Core Set of Shade-Avoidance Genes in Arabidopsis

The presence of neighboring vegetation modifies the light input perceived by photo-sensory receptors, initiating a signaling cascade that adjusts plant growth and physiology. Thousands of genes can change their expression during this process, but the structure of the transcriptional circuit is poorly understood. Here we present a meta-analysis of transcriptome data from Arabidopsis thaliana exposed to neighbor signals in different contexts, including organs where growth is promoted or inhibited by these signals. We identified a small set of genes that consistently and dynamically respond to neighbor light signals. This group is also affected by light during de-etiolation and day/night cycles. Among these genes, many of those with positive response to neighbor signals are binding targets of PHYTOCHROME-INTERACTING FACTORS (PIFs) and function as transcriptional regulators themselves, but none of these features is observed among those with negative response to neighbor signals. Changes. in neighbor signals can mimic the transcriptional signature of auxin, gibberellins, brassinosteroid, abscisic acid, ethylene, jasmonic acid and cytokinin but in a context-dependent manner. We propose the existence of a small core set of genes involved in downstream communication of PIF signaling status and in the control of light sensitivity and chloroplast metabolism.Fil: Sellaro, Romina Vanesa. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura; ArgentinaFil: Pacín, Manuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura; ArgentinaFil: Casal, Jorge José. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentin