Zea mays Transcriptome or Gene expression. Zea mays

Mutant maize lines expressing RNAi gene silencing constructs directed to two distinct classes of chromatin associated proteins show heightened sensitivity to UV-B including sunburned necrosis and down regulation of chromatin genes (Casati and Walbot, 2006). We have available transgenic maize expressing an RNAi for these chromatin factors: a subunit of a chromatin remodeling complex R, which is a SWI2/SNF2-like protein containing a SNF2 N and a helicase C domain (CHC101, AI746001); and a methyl-CpG-binding protein (MDB101, AI737448). To better understand the processes that involve chromatin remodeling proteins in UV-B responses, we conducted transcriptome analysis of chromatin remodeling knockdown plants in under two radiation regimes: plants were illuminated with UV-B lamps using fixtures mounted 30 cm above the plants (Phillips, F40UVB 40 W and TL 20 W/12) for 8 h; leaf samples were collected immediately after the radiation treatment. The bulbs were covered with CA filters to exclude wavelengths lower than 280 nm (UV-B). As a control, the bulbs were covered with PE filters to exclude wavelengths lower than 320 nm (minus UV-B). We analyzed genes that are changed upon UV-B irradiation in the transgenic plants and compared to the responses in non transgenic plants. To differentiate between differences due to background specific genes expression, we used non-transgenic sibling as controls. For these experiments, we used Long oligonucleotides arrays from Agilent Technologies. These studies will help to dilucidate how alteration in chromatin remodeling protein proteins affect gene expression, and the transcriptome analysis will help to understand why transgenic plants are hypersensity to UV-B. Keywords: genetic modification-stress response Overall design: Array hybridizations were carried out according to the manufacturer's instructions. For the experiments, Agilent Technologies microarrays were used, they contained 43,451 maize 60-mer probes and each slide had the same pattern of probes in quadruplicate (4x44 version), that were used to hybridize independent biological samples. Specifically, each array was hybridized with two samples, each of 0.825 μg labeled target cRNA, for 17 hours at 60°C. The samples were hybridized in a double loop design arrangement, as described by Kerr and Churchill et (2001). Data were acquired with an Agilent G2565BA scanner. Hybridizations for all 12 comparisons were highly correlated as assessed from correlations between median signal intensities (r2 = 0.97 for both dyes; data not shown) and between log2 ratios of the signals (r2 = 0.94; data not shown). Each sample was analyzed using 4 different biological replicates, and were hybridize to different arrays.