Detection of Plant Transcription Factors Using Sensitive Silicon Photonic Crystal Protein Arrays

Transcription factors control important gene regulation networks, altering the expression of a wide variety of genes, including those of agronomic importance, while often expressing at only a low level themselves. This can make detecting transcription factor proteins difficult, as current high-throughput methods may not be sensitive enough. Photonic crystal (PC) devices, attached to glass microscope slides, provide an alternative substrate for printing protein microarrays which has greater sensitivity through a reduced signal-to-noise ratio as compared to glass alone. In the past we have achieved enhancement of low-expressed genes on cDNA arrays using photonic crystal slides. Now we have examined seven stages of germinated soybean cotyledons using nine proteins of varying abundance, including proteins containing the NAC transcription factor domain. Antibodies to synthetic peptides have been printed on both regular glass slides and silicon photonic crystal (SiPC) slides. The SiPC devices are more sensitive than the glass slides, detecting low-expressed proteins that are below background on the glass slides. These antibodies have also been used in chromatin immunoprecipitation sequencing (ChIP-Seq) experiments to find the binding sites and confirm NAC activity; see Shamimuzzaman and Vodkin (2013) BMC Genomics and their poster at this meeting. Additionally, we have examined RNA-Seq data from these same tissues to compare the expression levels of mRNA and protein. Our future goals are to determine the limits of detection of this technology using lower concentrations of proteins and to examine new proteins of importance in seed development using this technology.